diff --git a/docs/build/doctrees/documentations.doctree b/docs/build/doctrees/documentations.doctree
index d820a6a..5f5d4a3 100644
Binary files a/docs/build/doctrees/documentations.doctree and b/docs/build/doctrees/documentations.doctree differ
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
index c91ed45..d9e4b26 100644
Binary files a/docs/build/doctrees/environment.pickle and b/docs/build/doctrees/environment.pickle differ
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
index 33987b9..a312773 100644
Binary files a/docs/build/doctrees/index.doctree and b/docs/build/doctrees/index.doctree differ
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
index 8ffd871..cf28314 100644
--- a/docs/build/html/.buildinfo
+++ b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 71c3667afe7096ee3bfc9c1417ac3e30
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: bb4c2dfbf28a34bc9897b378d59a51d7
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_sources/documentations.rst.txt b/docs/build/html/_sources/documentations.rst.txt
index 0e64e99..26fe015 100644
--- a/docs/build/html/_sources/documentations.rst.txt
+++ b/docs/build/html/_sources/documentations.rst.txt
@@ -16,13 +16,14 @@ Installation
 Dependencies
 ------------
 TreeProfiler requires 
-  - Python version >= 3.9
+  - Python version >= 3.10
   - ETE Toolkit v4
-  - biopython
-  - selenium
-  - scipy
-  - matplotlib
-  - numba
+  - biopython >= 1.8
+  - selenium >= 4.24
+  - scipy >= 1.8.0
+  - matplotlib >= 3.4
+  - pymc >= 5.0.0
+  - aesara
   - pastml (custom)
 
 Quick install via pip
@@ -32,8 +33,9 @@ Quick install via pip
     # Install ETE Toolkit v4
     pip install --force-reinstall https://github.com/etetoolkit/ete/archive/ete4.zip
 
+
     # Install TreeProfiler dependencies
-    pip install biopython selenium scipy matplotlib numba
+    pip install biopython selenium scipy matplotlib pymc aesara
 
     # Install custom pastml package for ete4
     pip install "git+https://github.com/dengzq1234/pastml.git@pastml2ete4" 
@@ -41,7 +43,7 @@ Quick install via pip
     # Install TreeProfiler tool via pip
     pip install TreeProfiler
 
-    # or installing main repo
+    # Or install directly from github
     pip install https://github.com/compgenomicslab/TreeProfiler/archive/main.zip
     # or development mode for latestest update
     pip install git+https://github.com/compgenomicslab/TreeProfiler@dev-repo
@@ -119,7 +121,7 @@ To install ETE in a local directory to help with the development, you can:
 - Install dependecies
   - If you are using conda: 
 
-  ``conda install -c conda-forge cython bottle brotli numpy pyqt``
+  ``conda install -c conda-forge cython bottle brotli pyqt numpy<2.0``
   
   - Otherwise, you can install them with 
   
@@ -137,7 +139,7 @@ Install dependencies
 ::
 
     # install BioPython, selenium, scipy via conda
-    conda install -c conda-forge biopython selenium scipy matplotlib
+    conda install -c conda-forge biopython selenium scipy matplotlib pymc
 
     # or pip
     pip install biopython selenium scipy matplotlib
@@ -154,7 +156,7 @@ or install inrectly from github
 ::
 
     # install directly
-    pip install https://github.com/dengzq1234/TreeProfiler/archive/refs/tags/v1.1.0.tar.gz
+    pip install https://github.com/compgenomicslab/TreeProfiler/archive/main.zip
 
 Input files
 -----------
@@ -196,61 +198,6 @@ The second subcommand ``plot`` is used to visualize tree with associated metadat
 Using TreeProfiler
 ==================
 In this Tutorial we will use TreeProfiler and demostrate basic usage with data in ``examples/``
-::
-
-    tree examples/
-    examples/
-    ├── automatic_query
-    │   ├── basic_example1_metadata1.tsv
-    │   ├── basic_example1.nw
-    │   ├── collapse_demo.sh
-    │   ├── highlight_demo.sh
-    │   └── prune_demo.sh
-    ├── basic_example1
-    │   ├── basic_example1_metadata1.tsv
-    │   ├── basic_example1_metadata2.tsv
-    │   ├── basic_example1.nw
-    │   └── example1_demo.sh
-    ├── basic_example2
-    │   ├── diauxic.array
-    │   ├── diauxic.nw
-    │   ├── example2_demo.sh
-    │   ├── FluA_H3_AA.fas
-    │   ├── MCC_FluA_H3_Genotype.txt
-    │   └── MCC_FluA_H3.nw
-    ├── pratical_example
-    │   ├── emapper
-    │   │   ├── 7955.ENSDARP00000116736.aln.faa
-    │   │   ├── 7955.ENSDARP00000116736.nw
-    │   │   ├── 7955.out.emapper.annotations
-    │   │   ├── 7955.out.emapper.pfam
-    │   │   ├── 7955.out.emapper.smart.out
-    │   │   ├── emapper_demo.sh
-    │   │   ├── nifH.faa.aln
-    │   │   ├── nifH.nw
-    │   │   ├── nifH.out.emapper.annotations
-    │   │   └── nifH.out.emapper.pfam
-    │   ├── gtdb_r202
-    │   │   ├── ar122_metadata_r202_lite.tar.gz
-    │   │   ├── bac120_metadata_r202_lite.tar.gz
-    │   │   ├── gtdbv202full_demo.sh
-    │   │   ├── gtdbv202lite_demo.sh
-    │   │   ├── gtdbv202.nw
-    │   │   ├── merge_gtdbtree.py
-    │   │   └── progenome3.tar.gz
-    │   └── progenome3
-    │       ├── progenome3.nw
-    │       ├── progenome3.tsv
-    │       └── progenome_demo.sh
-    └── taxonomy_example
-        ├── gtdb
-        │   ├── gtdb_demo.sh
-        │   ├── gtdb_example1.nw
-        │   └── gtdb_example1.tsv
-        └── ncbi
-            ├── ncbi_demo.sh
-            ├── ncbi_example.nw
-            └── ncbi_example.tsv
 
 Reading input tree
 ------------------
@@ -876,10 +823,9 @@ Using ``--column-summary-method``  can specify the summary method of each proper
 
 such as ``--column-summary-method sample1=none sample2=avg random_type=relative alignment=none``
 
-Noted that ``--data-matrix`` can be effected by ``--column-summary-method `` setting, in this case filename of the data matrix is property name, such as ``--data-matrix file.tsv --column-summary-method file.tsv=avg``
+Noted that ``--data-matrix`` can be effected by ``--column-summary-method`` setting, in this case filename of the data matrix is property name, such as ``--data-matrix file.tsv --column-summary-method file.tsv=avg``
 
-example:
-here we use three different metadata: ``categorical.tsv``, ``numerical.tsv`` and ``data matrix``
+example, here we use three different metadata: ``categorical.tsv``, ``numerical.tsv`` and ``data matrix``
 ::
 
   # cusomtize different summary methods for different column/property
@@ -1085,25 +1031,36 @@ When Taxon properties are embeded in different column or field in metadata, tree
 .. list-table:: 
    :header-rows: 1
 
-   * - metadata
+   * - metadata (`,` as column seperator)
      - taxon to be identified
      - command line setting
-   * - ``#leafname col1\n9598 wt``
+   * - ``#leafname,col1``
+       ``9598,wt``
      - 9598
-     - ``default``
-   * - ``#leafname col1\n7739.XP_002609184.1 wt``
+     - ``--taxon-column name``
+   * - ``#leafname,col1``
+       
+       ``7739.XP_002609184.1,wt``
      - 7739
-     - ``--taxon-column <default> --taxon-delimiter . --taxa-field 0``
-   * - ``#leafname ncbi_id\nleaf_A 7739``
+     - ``--taxon-column name --taxon-delimiter . --taxa-field 0``
+   * - ``#leafname,ncbi_id``
+
+       ``leaf_A,7739``
      - 7739
-     - ``--taxon-column ncbi_id --taxon-delimiter <default> --taxa-field <default>``
-   * - ``#leafname ncbi_id\nleaf_A 7739.XP_002609184.1``
+     - ``--taxon-column ncbi_id --taxon-delimiter . --taxa-field 0``
+   * - ``#leafname,ncbi_id``
+
+       ``leaf_A,7739.XP_002609184.1``
      - 7739
      - ``--taxon-column ncbi_id --taxon-delimiter . --taxa-field 0``
-   * - ``#leafname col1\nRS_GCF_001560035.1 wt``
+   * - ``#leafname,col1``
+
+       ``RS_GCF_001560035.1,wt``
      - RS_GCF_001560035.1
      - ``default``
-   * - ``#leafname gtdb_id\nleaf_A d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__Kariarchaeaceae;g__LC-2;s__LC-2 sp001940725``
+   * - ``#leafname,gtdb_id`` 
+       
+       ``leaf_A,d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__Kariarchaeaceae;g__LC-2;s__LC-2 sp001940725``
      - s__LC-2 sp001940725
      - ``--taxon-column gtdb_id --taxon-delimiter ; --taxa-field -1``
 
@@ -1407,12 +1364,21 @@ treeprofiler has integrated [pastml](https://github.com/evolbioinfo/pastml), a f
      - Description
    * - ``--acr-discrete-columns ACR_DISCRETE_COLUMNS [ACR_DISCRETE_COLUMNS ...]``
      - names of columns to perform acr analysis for discrete traits
-   * - ``--prediction-method {MPPA,MAP,JOINT,DOWNPASS,ACCTRAN,DELTRAN,COPY,ALL,ML,MP}``
-     - Prediction method for ACR discrete analysis. Options: MPPA, MAP, JOINT, DOWNPASS, ACCTRAN, DELTRAN, COPY, ALL, ML, MP. `[Default: MPPA]`
-   * - ``--model {JC, F81, EFT, HKY, JTT}``
-     - Evolutionary model for ML methods in ACR discrete analysis. Options: JC, F81, EFT, HKY, JTT. `[Default: F81]`
+   * - ``--acr-continuous-columns ACR_CONTINUOUS_COLUMNS [ACR_CONTINUOUS_COLUMNS ...]``
+     - names of columns to perform acr analysis for continuous traits
+   * - ``--prediction-method {MPPA,MAP,JOINT,DOWNPASS,ACCTRAN,DELTRAN,COPY,ALL,MP,ML,BAYESIAN}``
+     - Prediction method for ACR analysis.  
+       For **Discrete** traits: ``MPPA``, ``MAP``, ``JOINT``, ``DOWNPASS``, ``ACCTRAN``, ``DELTRAN``, ``COPY``, ``ALL``, ``ML``, ``MP``.  
+       For **Continuous** traits: ``ML``, ``BAYESIAN``.  
+       ``[Default: MPPA]``
+   * - ``--model {JC,F81,EFT,HKY,JTT,BM,OU}``
+     - Evolutionary model for ML methods in ACR analysis.  
+       For **discrete traits**: ``JC``, ``F81``, ``EFT``, ``HKY``, ``JTT``  
+       For **continuous traits**: ``BM``, ``OU``.  
+       ``[Default: F81]``
    * - ``--threads THREADS``
-     - Number of threads to use for annotation. `[Default: 4]`
+     - Number of threads to use for annotation.  
+       ``[Default: 4]``
 
 
 Example:
@@ -1664,6 +1630,77 @@ Delta statistic Examples
     'Country': 'Africa'
     }
 
+ACR for contiunous data
+^^^^^^^^^^^^^^^^^^^^^^^
+TreeProfiler supports ancestral character reconstruction for continuous traits using two main approaches: **Maximum Likelihood (ML)** and **Bayesian** inference. Both methods rely on evolutionary models for continuous data, specifically the **Brownian Motion (BM)** and **Ornstein-Uhlenbeck (OU)** models.
+
+TreeProfiler allows users to select the desired method and model using the following arguments:
+
+- ``--acr-continuous-columns <PROP>``: Specify the column names for the continuous traits.
+- ``--prediction-method <ML/BAYESIAN>``: Choose between the ML or Bayesian approach.
+- ``--model <BM/OU>``: Choose the evolutionary model for continuous trait analysis.
+
+Here is tree with example metadata which is continuous dataset ``Anolis.tre`` and ``svl.csv``:
+::
+  
+    head svl.csv
+    species,svl
+    ahli,4.039125443
+    alayoni,3.815704818
+    alfaroi,3.526654599
+    aliniger,4.036556538
+    allisoni,4.375390078
+
+    # now we run the acr for the continuous trait svl, here we turn off the descriptive statistic
+    treeprofiler annotate \
+    -t Anolis.tre \
+    --metadata svl.csv \
+    -s , \
+    --acr-continuous-columns svl \
+    --prediction-method ML \
+    --model BM \
+    --num-stat none \
+    -o ./
+
+    # now we check the 
+    python show_tree_props.py Anolis_annotated.nw
+    Target tree internal node Root contains the following properties:  
+    {
+      'name': 'Root', 
+      'svl': '4.065917563705425', 
+    }
+    Target tree leaf node ahlicontains the following propertiies:  
+    {
+      'name': 'ahli', 
+      'dist': 0.130889, 
+      'svl': '4.039125443'
+    }
+
+    # use Bayesian method with OU model
+    treeprofiler annotate \
+    -t Anolis.tre \
+    --metadata svl.csv \
+    -s , \
+    --acr-continuous-columns svl \
+    --prediction-method BAYESIAN \
+    --model OU \
+    --num-stat none \
+    -o ./
+
+    python show_tree_props.py Anolis_annotated.nw
+    Target tree internal node Root contains the following properties:  
+    {
+      'name': 'Root', 
+      'svl': '4.443782202699844'
+    }
+    Target tree leaf node ahlicontains the following propertiies:  
+    {
+      'name': 'ahli', 
+      'dist': 0.130889, 
+      'svl': '4.039125443'
+    }
+
+
 Lineage specificity analysis
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Using ``--ls-columns <prop_name>`` to start the lineage specificity analysis of boolean traits, the given trait need to be boolean value such as ``True`; ``False``; ``yes``; ``no``; ``t``; ``f``; ``1``; ``0``;  which fit the criteria in treeprofiler annotate. Calculated results will be stored in each internal nodes with suffix of ``_prec`` , ``_sens`` and ``_f1``.
@@ -1726,6 +1763,34 @@ In the following ``plot`` step, users can use either ``.nw`` or ``.ete`` by putt
 
  - ete format is a novel format developed to solve the situation we encounter in the previous step, annotated tree can be **recover easily with all the annotated data without changing the data type**. Besides, the ete format optimized the tree file size after mapped with its associated data. Hence it's very handy for programers in their own script. At this moment we can only view the ete format in treeprofiler, but we will make the ete format more universal to other phylogenetic software. **Hence using ete format in `plot` subcommand is highly reccomended**
 
+Use standard input and output formats
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+TreeProfiler is able to receive and produce trees in standard formats in order to integrate with command-line programs.
+
+- Standard output: Use ``--quiet`` and ``--stdout`` at the same time to mute the log and output the annotated tree in Newick format.
+
+::
+
+    cd basic_example0/
+    treeprofiler annotate \
+    -t demo1.tree \
+    --metadata categorical.tsv \
+    -s , \
+    --quiet \
+    --stdout
+
+    ((Taxa_3:0.219065[&&NHX:categorical1=C],(Taxa_4:0.188681[&&NHX:categorical1=C],Taxa_2:0.5196[&&NHX:categorical1=B])0.166914:0.90365[&&NHX:categorical1_counter=B--1||C--1:name=N3])0.138062:0.0632016[&&NHX:categorical1_counter=B--1||C--2:name=N4],(Taxa_0:0.190563[&&NHX:categorical1=A],Taxa_1:0.458423[&&NHX:categorical1=B])0.138062:0.97338[&&NHX:categorical1_counter=A--1||B--1:name=N7])[&&NHX:categorical1_counter=A--1||B--2||C--2:name=Root];
+
+- Standard input, use ``-`` as input in ``--tree`` argument to take standard input into account.
+
+::
+
+    cd basic_example0/
+
+    cat demo1.tree|treeprofiler annotate -t - --metadata categorical.tsv -s , --quiet --stdout
+
+    ((Taxa_3:0.219065[&&NHX:categorical1=C],(Taxa_4:0.188681[&&NHX:categorical1=C],Taxa_2:0.5196[&&NHX:categorical1=B])0.166914:0.90365[&&NHX:categorical1_counter=B--1||C--1:name=N3])0.138062:0.0632016[&&NHX:categorical1_counter=B--1||C--2:name=N4],(Taxa_0:0.190563[&&NHX:categorical1=A],Taxa_1:0.458423[&&NHX:categorical1=B])0.138062:0.97338[&&NHX:categorical1_counter=A--1||B--1:name=N7])[&&NHX:categorical1_counter=A--1||B--2||C--2:name=Root];
+
 ``treeprofiler-plot`` visualizing phylogenetic profiles and annotation
 ------------------------------------------------------------------------- 
 The ``plot`` command can be used to visually explore any annotated tree produced by the
@@ -1811,8 +1876,7 @@ Examples with basic parameters:
 
 Layouts for categorical data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Users can add the following flag to activate layouts for categorical data
+Users can add the following flag to activate layouts for categorical data.
 
 .. list-table:: 
    :header-rows: 1
@@ -1833,6 +1897,10 @@ Users can add the following flag to activate layouts for categorical data
      - ``<prop1> <prop2>`` names of properties where branches will be colored based on different values.
      - Branch with color
      - Stacked Horizontal RecFace (only collapsed)
+   * - ``--bubble-layout BUBBLE_LAYOUT [BUBBLE_LAYOUT ...]``
+     - ``<prop1> <prop2>`` names of properties where nodes will be colored based on different bubble.
+     - Circles with color
+     - None
    * - ``--background-layout BACKGROUND_LAYOUT [BACKGROUND_LAYOUT ...]``
      - ``<prop1> <prop2>`` names of properties where values will be labeled as rectangular color blocks on the aligned panel.
      - Background with color
@@ -1909,6 +1977,19 @@ If internal node doesn't have the given property, once it collapsed,  aligned pa
 .. image:: https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_colorbranch_layout_random.png?raw=true
     :alt: colorbranch_layout example
 
+Bubble Layout
+^^^^^^^^^^^^^^
+``--bubble-layout`` categorizes values of selected property by displaying color bubble on the corresponing leaf node.
+
+::
+
+    treeprofiler plot \
+    -t basic_example1_annotated.ete \
+    --bubble-layout random_type
+
+.. image:: https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_bubble_layout_randomtype.png?raw=true
+    :alt: bubble_layout example
+
 Background Layout
 ^^^^^^^^^^^^^^^^^
 ``--background-layout`` works just like ``--colorbranch-layout``, the only difference is ``--background-layout`` visualize the background of the corresponding node instead of the branch color. It is useful and more visual when the tree is large.
@@ -2251,6 +2332,9 @@ Barplot Layout
 
 ``--barplot-scale`` is the parameter to set the scale of barplot, if not given, the scale will be the maximum value of the property.
 
+``--barplot-colorby`` set the color of barplot by the a categorical property from metadata.[default: None]
+
+
 Examples:
 ::
 
@@ -2286,6 +2370,21 @@ Examples:
 .. image:: https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_barplot_layout3.png?raw=true
     :alt: barplot_layout3 example
 
+
+Noticed barplot in general is filled with one color for each column, using `--barplot-colorby` allows users to fill barplot based on other categorical data.
+
+here we color barplot ``abs_data`` by the categorical data ``random_type``
+
+::
+
+    treeprofiler plot \
+    -t basic_example1_annotated.ete \
+    --barplot-layout abs_data \
+    --barplot-colorby random_type
+
+.. image:: https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_barplot_layout4.png?raw=true
+    :alt: barplot_layout4 example
+
 Numerical Matrix Layout
 ^^^^^^^^^^^^^^^^^^^^^^^^
 ``--numerical-matrix-layout`` is similar to ``--heatmap-layout`` but using draw_array from ete4 therefore it is suitable for large scale, and also visualize data matrix which was stored as a file in previous annotation step.. But the limit is only work on rectangular tree.
@@ -2341,9 +2440,11 @@ Users can add the following arguments to use layouts for Analytical data
    * - Argument
      - Description
    * - ``--acr-discrete-layout ACR_DISCRETE_LAYOUT [ACR_DISCRETE_LAYOUT ...]``
-     - <prop1> <prop2> names of properties which need to be plotted as acr-discrete-layout.
+     - ``<prop1> <prop2>`` names of properties that need to be plotted as acr-discrete-layout.
+   * - ``--acr-continuous-layout ACR_CONTINUOUS_LAYOUT [ACR_CONTINUOUS_LAYOUT ...]``
+     - ``<prop1> <prop2>`` names of properties that need to be plotted as acr-continuous-layout.
    * - ``--ls-layout LS_LAYOUT [LS_LAYOUT ...]``
-     - <prop1> <prop2> names of properties which need to be plotted as ls-layout.
+     - ``<prop1> <prop2>`` names of properties that need to be plotted as ls-layout.
 
 We use example from `examples/analytic_example`:
 ::
@@ -2402,6 +2503,30 @@ We use example from `examples/analytic_example`:
 .. image:: https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_ls_layout2.png?raw=true
     :alt: ls_layout example
 
+Ancestral Character Reconstruction for continuous traits
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Computing ACR for continuous traits:
+
+::
+
+    treeprofiler annotate \
+    -t Anolis.tre \
+    --metadata svl.csv \
+    -s , \
+    --acr-continuous-columns svl \
+    --prediction-method BAYESIAN \
+    --model OU \
+    --num-stat none \
+    -o ./
+
+
+    treeprofiler plot \
+    -t Anolis_annotated.ete \
+    --acr-continuous-layout svl
+
+.. image:: https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_acr_continuous_layout.png?raw=true
+    :alt: acr_continuous_layout example
+
 Layouts for Multiple Sequence Alignment
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 In order to visualize multiple sequence alignment alongside with the tree, first we need to annotate alignment using ``--alignment`` in ``annotate``. Then activate alignment layout by adding ``--alignment-layout``. Consensus sequence (if calculated) will shown once internal nodes collapsed.
@@ -3122,6 +3247,90 @@ OR condition will be used more than one arguments:
 .. image:: https://github.com/dengzq1234/treeprofiler_gallery/blob/main/highlighted_or.png?raw=true
    :alt: highlighted_or
 
+Conditional query with config file
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+In conditinary query, it also accept to use config to customize the highlighted and collapsed visualization. Example config file in `color.config.template`. It has the same structure as color config but the CONDITION column here is for operators as we mentioned in previous session.
+
+::
+
+    cat color.config.template`
+    # TreeProfiler Conditional query Configuration
+    # This file defines custom colors for properties of annotated tree nodes.
+    # Columns: PROP, VALUE, COLOR, CONDITION
+
+    # PROP: Property of the annotated tree node
+    # VALUE: Value of the property to be colored
+    # COLOR: Color to apply
+    # CONDITION: operator
+
+    PROP,VALUE,COLOR,CONDITION
+
+Highlight with custom config
+'''''''''''''''''''''''''''''
+we use example of ``basic_example1.nw`` and ``basic_example1_metadata1.tsv``, we hope to highlight nodes whose `random_type` is `low` AND `sample1` greater than `0.50`, and we want to highlight those nodes in red. 
+
+First we customize the config ``color.config.query``:
+
+::
+
+    # TreeProfiler Conditional query Configuration
+    # This file defines custom colors for properties of annotated tree nodes.
+    # Columns: PROP, VALUE, COLOR, CONDITION
+
+    # PROP: Property of the annotated tree node
+    # VALUE: Value of the property to be colored
+    # COLOR: Color to apply
+    # CONDITION: operator
+
+    PROP,VALUE,COLOR,CONDITION
+    random_type,low,red,=
+    sample1,0.50,red,>
+
+we attach the config using the same ``--highlighted-by``, dont forget about the ``-s`` to indicate the seperator
+
+::
+
+    treeprofiler plot \
+    -t basic_example1_annotated.ete \
+    --highlighted-by color.config.query \
+    -s ,
+
+.. image:: https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_query_config1.png?raw=true
+    :alt: highlighted_query
+
+
+Collapse with custom config
+'''''''''''''''''''''''''''''
+Similar to ``--highlighted-by``, in this case we try to collapse the internal nodes whose average of leaf properties `sample1` greater than `0.50`, with color of green. 
+
+The config is in ``color.config.collapsed``
+
+::
+
+    # TreeProfiler Conditional query Configuration
+    # This file defines custom colors for properties of annotated tree nodes.
+    # Columns: PROP, VALUE, COLOR, CONDITION
+
+    # PROP: Property of the annotated tree node
+    # VALUE: Value of the property to be colored
+    # COLOR: Color to apply
+    # CONDITION: operator
+
+    PROP,VALUE,COLOR,CONDITION
+    #random_type_counter:high,0.35,red,>
+    sample1_avg,0.50,green,>
+
+example run 
+::
+
+    treeprofiler plot \
+    -t basic_example1_annotated.ete \
+    --collapsed-by color.config.collapsed \
+    -s ,
+
+.. image::https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_query_config2.png?raw=true 
+  :alt: collapse_query
+
 Conditional limit based on taxonomic level
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Prune taxonomic annotated tree based on following taxonomic rank level,
diff --git a/docs/build/html/documentations.html b/docs/build/html/documentations.html
index 17b248b..53ea9a0 100644
--- a/docs/build/html/documentations.html
+++ b/docs/build/html/documentations.html
@@ -6,16 +6,17 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>TreeProfiler Tutorial &#8212; treeprofiler [1.2.2-beta] documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d1102ebc" />
-    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=12dfc556" />
-    <script src="_static/documentation_options.js?v=fbc843e6"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
-    <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+    <link rel="stylesheet" type="text/css" href="static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="static/basic.css?v=686e5160" />
+    <link rel="stylesheet" type="text/css" href="static/alabaster.css?v=27fed22d" />
+    <script src="static/documentation_options.js?v=fbc843e6"></script>
+    <script src="static/doctools.js?v=9bcbadda"></script>
+    <script src="static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="prev" title="Welcome to treeprofiler’s documentation!" href="index.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
   
 
   
@@ -32,204 +33,219 @@
           <div class="body" role="main">
             
   <section id="treeprofiler-tutorial">
-<h1><a class="toc-backref" href="#id3" role="doc-backlink">TreeProfiler Tutorial</a><a class="headerlink" href="#treeprofiler-tutorial" title="Link to this heading">¶</a></h1>
+<h1><a class="toc-backref" href="#id4" role="doc-backlink">TreeProfiler Tutorial</a><a class="headerlink" href="#treeprofiler-tutorial" title="Link to this heading">¶</a></h1>
 </section>
 <section id="introduction">
-<h1><a class="toc-backref" href="#id4" role="doc-backlink">Introduction</a><a class="headerlink" href="#introduction" title="Link to this heading">¶</a></h1>
+<h1><a class="toc-backref" href="#id5" role="doc-backlink">Introduction</a><a class="headerlink" href="#introduction" title="Link to this heading">¶</a></h1>
 <p>TreeProfiler is command-line tool for profiling metadata table into phylogenetic tree with descriptive analysis and output visualization</p>
 </section>
 <section id="table-of-contents">
-<h1><a class="toc-backref" href="#id5" role="doc-backlink">Table of Contents</a><a class="headerlink" href="#table-of-contents" title="Link to this heading">¶</a></h1>
+<h1><a class="toc-backref" href="#id6" role="doc-backlink">Table of Contents</a><a class="headerlink" href="#table-of-contents" title="Link to this heading">¶</a></h1>
 <nav class="contents" id="contents">
 <p class="topic-title">Contents</p>
 <ul class="simple">
-<li><p><a class="reference internal" href="#treeprofiler-tutorial" id="id3">TreeProfiler Tutorial</a></p></li>
-<li><p><a class="reference internal" href="#introduction" id="id4">Introduction</a></p></li>
-<li><p><a class="reference internal" href="#table-of-contents" id="id5">Table of Contents</a></p></li>
-<li><p><a class="reference internal" href="#installation" id="id6">Installation</a></p>
+<li><p><a class="reference internal" href="#treeprofiler-tutorial" id="id4">TreeProfiler Tutorial</a></p></li>
+<li><p><a class="reference internal" href="#introduction" id="id5">Introduction</a></p></li>
+<li><p><a class="reference internal" href="#table-of-contents" id="id6">Table of Contents</a></p></li>
+<li><p><a class="reference internal" href="#installation" id="id7">Installation</a></p>
 <ul>
-<li><p><a class="reference internal" href="#dependencies" id="id7">Dependencies</a></p></li>
-<li><p><a class="reference internal" href="#quick-install-via-pip" id="id8">Quick install via pip</a></p></li>
-<li><p><a class="reference internal" href="#quick-start-with-examples-dataset" id="id9">Quick Start with examples dataset</a></p></li>
-<li><p><a class="reference internal" href="#manual-installation" id="id10">Manual installation</a></p>
+<li><p><a class="reference internal" href="#dependencies" id="id8">Dependencies</a></p></li>
+<li><p><a class="reference internal" href="#quick-install-via-pip" id="id9">Quick install via pip</a></p></li>
+<li><p><a class="reference internal" href="#quick-start-with-examples-dataset" id="id10">Quick Start with examples dataset</a></p></li>
+<li><p><a class="reference internal" href="#manual-installation" id="id11">Manual installation</a></p>
 <ul>
-<li><p><a class="reference internal" href="#install-ete-v4" id="id11">Install ETE v4</a></p></li>
-<li><p><a class="reference internal" href="#install-treeprofiler" id="id12">Install TreeProfiler</a></p></li>
+<li><p><a class="reference internal" href="#install-ete-v4" id="id12">Install ETE v4</a></p></li>
+<li><p><a class="reference internal" href="#install-treeprofiler" id="id13">Install TreeProfiler</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#input-files" id="id13">Input files</a></p></li>
-<li><p><a class="reference internal" href="#basic-usage" id="id14">Basic Usage</a></p></li>
+<li><p><a class="reference internal" href="#input-files" id="id14">Input files</a></p></li>
+<li><p><a class="reference internal" href="#basic-usage" id="id15">Basic Usage</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#using-treeprofiler" id="id15">Using TreeProfiler</a></p>
+<li><p><a class="reference internal" href="#using-treeprofiler" id="id16">Using TreeProfiler</a></p>
 <ul>
-<li><p><a class="reference internal" href="#reading-input-tree" id="id16">Reading input tree</a></p>
+<li><p><a class="reference internal" href="#reading-input-tree" id="id17">Reading input tree</a></p>
 <ul>
-<li><p><a class="reference internal" href="#tree-format" id="id17">Tree format</a></p></li>
-<li><p><a class="reference internal" href="#tree-parser" id="id18">Tree parser</a></p></li>
+<li><p><a class="reference internal" href="#tree-format" id="id18">Tree format</a></p></li>
+<li><p><a class="reference internal" href="#tree-parser" id="id19">Tree parser</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#treeprofiler-annotate-computing-phylogenetic-profiles-and-annotation" id="id19"><code class="docutils literal notranslate"><span class="pre">treeprofiler-annotate</span></code> computing phylogenetic profiles and annotation</a></p>
+<li><p><a class="reference internal" href="#treeprofiler-annotate-computing-phylogenetic-profiles-and-annotation" id="id20"><code class="docutils literal notranslate"><span class="pre">treeprofiler-annotate</span></code> computing phylogenetic profiles and annotation</a></p>
 <ul>
-<li><p><a class="reference internal" href="#annotate-metadata-into-tree" id="id20">Annotate metadata into tree</a></p>
+<li><p><a class="reference internal" href="#annotate-metadata-into-tree" id="id21">Annotate metadata into tree</a></p>
 <ul>
-<li><p><a class="reference internal" href="#basic-metadata-in-tsv-csv-format" id="id21">Basic metadata in TSV/CSV format</a></p></li>
-<li><p><a class="reference internal" href="#metadata-tsv-csv-as-a-numerical-data-matrix" id="id22">Metadata TSV/CSV as a numerical data matrix</a></p></li>
-<li><p><a class="reference internal" href="#metadata-without-column-names" id="id23">Metadata without column names</a></p></li>
-<li><p><a class="reference internal" href="#missing-value-detection" id="id24">Missing value detection</a></p></li>
-<li><p><a class="reference internal" href="#unmapped-tree-leaf-property-detection" id="id25">Unmapped tree leaf property detection</a></p></li>
-<li><p><a class="reference internal" href="#handling-duplicated-leaf-names-in-metadata" id="id26">Handling duplicated leaf names in metadata</a></p></li>
-<li><p><a class="reference internal" href="#specifying-data-types-for-metadata-columns" id="id27">Specifying data types for metadata columns</a></p></li>
-<li><p><a class="reference internal" href="#annotate-metadata-to-internal-nodes" id="id28">Annotate metadata to internal nodes</a></p>
+<li><p><a class="reference internal" href="#basic-metadata-in-tsv-csv-format" id="id22">Basic metadata in TSV/CSV format</a></p></li>
+<li><p><a class="reference internal" href="#metadata-tsv-csv-as-a-numerical-data-matrix" id="id23">Metadata TSV/CSV as a numerical data matrix</a></p></li>
+<li><p><a class="reference internal" href="#metadata-without-column-names" id="id24">Metadata without column names</a></p></li>
+<li><p><a class="reference internal" href="#missing-value-detection" id="id25">Missing value detection</a></p></li>
+<li><p><a class="reference internal" href="#unmapped-tree-leaf-property-detection" id="id26">Unmapped tree leaf property detection</a></p></li>
+<li><p><a class="reference internal" href="#handling-duplicated-leaf-names-in-metadata" id="id27">Handling duplicated leaf names in metadata</a></p></li>
+<li><p><a class="reference internal" href="#specifying-data-types-for-metadata-columns" id="id28">Specifying data types for metadata columns</a></p></li>
+<li><p><a class="reference internal" href="#annotate-metadata-to-internal-nodes" id="id29">Annotate metadata to internal nodes</a></p>
 <ul>
-<li><p><a class="reference internal" href="#customizing-summary-methods-for-different-columns" id="id29">Customizing summary methods for different columns</a></p></li>
+<li><p><a class="reference internal" href="#customizing-summary-methods-for-different-columns" id="id30">Customizing summary methods for different columns</a></p></li>
 </ul>
 </li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#taxonomic-annotation" id="id30">Taxonomic annotation</a></p>
+<li><p><a class="reference internal" href="#taxonomic-annotation" id="id31">Taxonomic annotation</a></p>
 <ul>
-<li><p><a class="reference internal" href="#using-different-taxonomic-databases-from-gtdb-ncbi" id="id31">Using different taxonomic databases from GTDB/NCBI</a></p></li>
-<li><p><a class="reference internal" href="#identifying-taxon-names-in-different-metadata-fields-columns" id="id32">Identifying taxon names in different metadata fields/columns</a></p></li>
-<li><p><a class="reference internal" href="#ignoring-unclassified-taxonomic-annotations" id="id33">Ignoring unclassified taxonomic annotations</a></p></li>
+<li><p><a class="reference internal" href="#using-different-taxonomic-databases-from-gtdb-ncbi" id="id32">Using different taxonomic databases from GTDB/NCBI</a></p></li>
+<li><p><a class="reference internal" href="#identifying-taxon-names-in-different-metadata-fields-columns" id="id33">Identifying taxon names in different metadata fields/columns</a></p></li>
+<li><p><a class="reference internal" href="#ignoring-unclassified-taxonomic-annotations" id="id34">Ignoring unclassified taxonomic annotations</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#functional-annotation" id="id34">Functional annotation</a></p>
+<li><p><a class="reference internal" href="#functional-annotation" id="id35">Functional annotation</a></p>
 <ul>
-<li><p><a class="reference internal" href="#annotating-multiple-sequence-alignments-msa" id="id35">Annotating Multiple Sequence Alignments(MSA)</a></p></li>
-<li><p><a class="reference internal" href="#annotating-eggnog-mapper-output-and-domain-information" id="id36">Annotating EggNOG-Mapper output and Domain information</a></p></li>
+<li><p><a class="reference internal" href="#annotating-multiple-sequence-alignments-msa" id="id36">Annotating Multiple Sequence Alignments(MSA)</a></p></li>
+<li><p><a class="reference internal" href="#annotating-eggnog-mapper-output-and-domain-information" id="id37">Annotating EggNOG-Mapper output and Domain information</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#analytical-methods-in-treeprofiler" id="id37">Analytical methods in treeProfiler</a></p>
+<li><p><a class="reference internal" href="#analytical-methods-in-treeprofiler" id="id38">Analytical methods in treeProfiler</a></p>
 <ul>
-<li><p><a class="reference internal" href="#ancestral-character-reconstruction" id="id38">Ancestral character reconstruction</a></p></li>
-<li><p><a class="reference internal" href="#phylogenetic-signal-delta-statistic" id="id39">Phylogenetic signal delta statistic</a></p></li>
-<li><p><a class="reference internal" href="#lineage-specificity-analysis" id="id40">Lineage specificity analysis</a></p></li>
+<li><p><a class="reference internal" href="#ancestral-character-reconstruction" id="id39">Ancestral character reconstruction</a></p></li>
+<li><p><a class="reference internal" href="#phylogenetic-signal-delta-statistic" id="id40">Phylogenetic signal delta statistic</a></p></li>
+<li><p><a class="reference internal" href="#acr-for-contiunous-data" id="id41">ACR for contiunous data</a></p></li>
+<li><p><a class="reference internal" href="#lineage-specificity-analysis" id="id42">Lineage specificity analysis</a></p></li>
+</ul>
+</li>
+<li><p><a class="reference internal" href="#output-formats-for-annotated-trees" id="id43">Output formats for annotated trees</a></p>
+<ul>
+<li><p><a class="reference internal" href="#use-standard-input-and-output-formats" id="id44">Use standard input and output formats</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#output-formats-for-annotated-trees" id="id41">Output formats for annotated trees</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#treeprofiler-plot-visualizing-phylogenetic-profiles-and-annotation" id="id42"><code class="docutils literal notranslate"><span class="pre">treeprofiler-plot</span></code> visualizing phylogenetic profiles and annotation</a></p>
+<li><p><a class="reference internal" href="#treeprofiler-plot-visualizing-phylogenetic-profiles-and-annotation" id="id45"><code class="docutils literal notranslate"><span class="pre">treeprofiler-plot</span></code> visualizing phylogenetic profiles and annotation</a></p>
 <ul>
-<li><p><a class="reference internal" href="#interactive-visualization-interface" id="id43">Interactive visualization interface</a></p></li>
-<li><p><a class="reference internal" href="#basic-options-of-visualizing-layouts" id="id44">Basic options of visualizing layouts</a></p></li>
-<li><p><a class="reference internal" href="#layouts-for-categorical-data" id="id45">Layouts for categorical data</a></p>
+<li><p><a class="reference internal" href="#interactive-visualization-interface" id="id46">Interactive visualization interface</a></p></li>
+<li><p><a class="reference internal" href="#basic-options-of-visualizing-layouts" id="id47">Basic options of visualizing layouts</a></p></li>
+<li><p><a class="reference internal" href="#layouts-for-categorical-data" id="id48">Layouts for categorical data</a></p>
 <ul>
-<li><p><a class="reference internal" href="#lable-layout" id="id46">Lable Layout</a></p></li>
-<li><p><a class="reference internal" href="#rectangle-layout" id="id47">Rectangle Layout</a></p></li>
-<li><p><a class="reference internal" href="#colorbranch-layout" id="id48">ColorBranch Layout</a></p></li>
-<li><p><a class="reference internal" href="#background-layout" id="id49">Background Layout</a></p></li>
-<li><p><a class="reference internal" href="#piechart-layout" id="id50">Piechart Layout</a></p></li>
-<li><p><a class="reference internal" href="#profiling-layout" id="id51">Profiling Layout</a></p></li>
-<li><p><a class="reference internal" href="#categorical-matrix-layout" id="id52">Categorical Matrix Layout</a></p></li>
+<li><p><a class="reference internal" href="#lable-layout" id="id49">Lable Layout</a></p></li>
+<li><p><a class="reference internal" href="#rectangle-layout" id="id50">Rectangle Layout</a></p></li>
+<li><p><a class="reference internal" href="#colorbranch-layout" id="id51">ColorBranch Layout</a></p></li>
+<li><p><a class="reference internal" href="#bubble-layout" id="id52">Bubble Layout</a></p></li>
+<li><p><a class="reference internal" href="#background-layout" id="id53">Background Layout</a></p></li>
+<li><p><a class="reference internal" href="#piechart-layout" id="id54">Piechart Layout</a></p></li>
+<li><p><a class="reference internal" href="#profiling-layout" id="id55">Profiling Layout</a></p></li>
+<li><p><a class="reference internal" href="#categorical-matrix-layout" id="id56">Categorical Matrix Layout</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#layouts-for-boolean-data" id="id53">Layouts for boolean data</a></p>
+<li><p><a class="reference internal" href="#layouts-for-boolean-data" id="id57">Layouts for boolean data</a></p>
 <ul>
-<li><p><a class="reference internal" href="#binary-layout" id="id54">Binary Layout</a></p></li>
-<li><p><a class="reference internal" href="#binary-aggregate-layout" id="id55">Binary Aggregate Layout</a></p></li>
-<li><p><a class="reference internal" href="#binary-unicolor-layout" id="id56">Binary Unicolor Layout</a></p></li>
-<li><p><a class="reference internal" href="#binary-unicolor-aggregate-layout" id="id57">Binary Unicolor Aggregate Layout</a></p></li>
-<li><p><a class="reference internal" href="#binary-matrix-layout" id="id58">Binary Matrix Layout</a></p></li>
+<li><p><a class="reference internal" href="#binary-layout" id="id58">Binary Layout</a></p></li>
+<li><p><a class="reference internal" href="#binary-aggregate-layout" id="id59">Binary Aggregate Layout</a></p></li>
+<li><p><a class="reference internal" href="#binary-unicolor-layout" id="id60">Binary Unicolor Layout</a></p></li>
+<li><p><a class="reference internal" href="#binary-unicolor-aggregate-layout" id="id61">Binary Unicolor Aggregate Layout</a></p></li>
+<li><p><a class="reference internal" href="#binary-matrix-layout" id="id62">Binary Matrix Layout</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#layouts-for-numerical-data" id="id59">Layouts for Numerical data</a></p>
+<li><p><a class="reference internal" href="#layouts-for-numerical-data" id="id63">Layouts for Numerical data</a></p>
 <ul>
-<li><p><a class="reference internal" href="#id1" id="id60">ColorBranch Layout</a></p></li>
-<li><p><a class="reference internal" href="#bubble-layout" id="id61">Bubble Layout</a></p></li>
-<li><p><a class="reference internal" href="#heatmap-layout" id="id62">Heatmap Layout</a></p></li>
-<li><p><a class="reference internal" href="#barplot-layout" id="id63">Barplot Layout</a></p></li>
-<li><p><a class="reference internal" href="#numerical-matrix-layout" id="id64">Numerical Matrix Layout</a></p></li>
+<li><p><a class="reference internal" href="#id1" id="id64">ColorBranch Layout</a></p></li>
+<li><p><a class="reference internal" href="#id2" id="id65">Bubble Layout</a></p></li>
+<li><p><a class="reference internal" href="#heatmap-layout" id="id66">Heatmap Layout</a></p></li>
+<li><p><a class="reference internal" href="#barplot-layout" id="id67">Barplot Layout</a></p></li>
+<li><p><a class="reference internal" href="#numerical-matrix-layout" id="id68">Numerical Matrix Layout</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#layouts-for-analytical-data" id="id65">Layouts for Analytical Data</a></p>
+<li><p><a class="reference internal" href="#layouts-for-analytical-data" id="id69">Layouts for Analytical Data</a></p>
 <ul>
-<li><p><a class="reference internal" href="#ancestral-character-reconstruction-and-phylogenetic-signal-layout" id="id66">Ancestral Character Reconstruction and Phylogenetic Signal Layout</a></p></li>
-<li><p><a class="reference internal" href="#lineage-specificity-layout" id="id67">Lineage Specificity Layout</a></p></li>
+<li><p><a class="reference internal" href="#ancestral-character-reconstruction-and-phylogenetic-signal-layout" id="id70">Ancestral Character Reconstruction and Phylogenetic Signal Layout</a></p></li>
+<li><p><a class="reference internal" href="#lineage-specificity-layout" id="id71">Lineage Specificity Layout</a></p></li>
+<li><p><a class="reference internal" href="#ancestral-character-reconstruction-for-continuous-traits" id="id72">Ancestral Character Reconstruction for continuous traits</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#layouts-for-multiple-sequence-alignment" id="id68">Layouts for Multiple Sequence Alignment</a></p></li>
-<li><p><a class="reference internal" href="#layouts-for-eggnog-mapper-pfam-smart-annotations" id="id69">Layouts for eggnog-mapper pfam/smart annotations</a></p></li>
-<li><p><a class="reference internal" href="#layouts-for-eggnog-mapper-functional-annotations" id="id70">Layouts for eggnog-mapper functional annotations</a></p></li>
-<li><p><a class="reference internal" href="#layouts-for-taxonomy-annotation" id="id71">Layouts for Taxonomy annotation</a></p>
+<li><p><a class="reference internal" href="#layouts-for-multiple-sequence-alignment" id="id73">Layouts for Multiple Sequence Alignment</a></p></li>
+<li><p><a class="reference internal" href="#layouts-for-eggnog-mapper-pfam-smart-annotations" id="id74">Layouts for eggnog-mapper pfam/smart annotations</a></p></li>
+<li><p><a class="reference internal" href="#layouts-for-eggnog-mapper-functional-annotations" id="id75">Layouts for eggnog-mapper functional annotations</a></p></li>
+<li><p><a class="reference internal" href="#layouts-for-taxonomy-annotation" id="id76">Layouts for Taxonomy annotation</a></p>
 <ul>
-<li><p><a class="reference internal" href="#taxonclade-layout" id="id72">TaxonClade Layout</a></p></li>
-<li><p><a class="reference internal" href="#taxonrectangle-layout" id="id73">TaxonRectangle Layout</a></p></li>
-<li><p><a class="reference internal" href="#taxoncollapse-layout" id="id74">TaxonCollapse Layout</a></p></li>
+<li><p><a class="reference internal" href="#taxonclade-layout" id="id77">TaxonClade Layout</a></p></li>
+<li><p><a class="reference internal" href="#taxonrectangle-layout" id="id78">TaxonRectangle Layout</a></p></li>
+<li><p><a class="reference internal" href="#taxoncollapse-layout" id="id79">TaxonCollapse Layout</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#customize-color-in-layout-with-color-config" id="id75">Customize color in layout with color config</a></p>
+<li><p><a class="reference internal" href="#customize-color-in-layout-with-color-config" id="id80">Customize color in layout with color config</a></p>
 <ul>
-<li><p><a class="reference internal" href="#basic-setting" id="id76">Basic setting</a></p>
+<li><p><a class="reference internal" href="#basic-setting" id="id81">Basic setting</a></p>
 <ul>
-<li><p><a class="reference internal" href="#customize-color-for-categorical-data" id="id77">Customize color for categorical data</a></p></li>
-<li><p><a class="reference internal" href="#customize-color-for-boolean-data" id="id78">Customize color for boolean data</a></p></li>
-<li><p><a class="reference internal" href="#customize-color-for-numerical-data" id="id79">Customize color for numerical data</a></p></li>
+<li><p><a class="reference internal" href="#customize-color-for-categorical-data" id="id82">Customize color for categorical data</a></p></li>
+<li><p><a class="reference internal" href="#customize-color-for-boolean-data" id="id83">Customize color for boolean data</a></p></li>
+<li><p><a class="reference internal" href="#customize-color-for-numerical-data" id="id84">Customize color for numerical data</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#advanced-setting" id="id80">Advanced Setting</a></p>
+<li><p><a class="reference internal" href="#advanced-setting" id="id85">Advanced Setting</a></p>
 <ul>
-<li><p><a class="reference internal" href="#setting-color-range-for-numerical-data" id="id81">Setting color range for numerical data</a></p></li>
-<li><p><a class="reference internal" href="#combining-settings-of-value-and-color-range-for-numerical-data" id="id82">Combining settings of value and color range for numerical data</a></p></li>
-<li><p><a class="reference internal" href="#wildcard-settings-of-color-range-for-numerical-matrix" id="id83">Wildcard settings of color range for numerical matrix</a></p></li>
-<li><p><a class="reference internal" href="#customize-color-settings-with-complex-conditions" id="id84">Customize color settings with complex conditions</a></p></li>
+<li><p><a class="reference internal" href="#setting-color-range-for-numerical-data" id="id86">Setting color range for numerical data</a></p></li>
+<li><p><a class="reference internal" href="#combining-settings-of-value-and-color-range-for-numerical-data" id="id87">Combining settings of value and color range for numerical data</a></p></li>
+<li><p><a class="reference internal" href="#wildcard-settings-of-color-range-for-numerical-matrix" id="id88">Wildcard settings of color range for numerical matrix</a></p></li>
+<li><p><a class="reference internal" href="#customize-color-settings-with-complex-conditions" id="id89">Customize color settings with complex conditions</a></p></li>
 </ul>
 </li>
 </ul>
 </li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#conditional-query-in-annotated-tree-can-be-used-in-both-annotate-and-plot" id="id85">Conditional query in annotated tree (can be used in both annotate and plot)</a></p>
+<li><p><a class="reference internal" href="#conditional-query-in-annotated-tree-can-be-used-in-both-annotate-and-plot" id="id90">Conditional query in annotated tree (can be used in both annotate and plot)</a></p>
 <ul>
-<li><p><a class="reference internal" href="#query-syntax" id="id86">Query Syntax</a></p>
+<li><p><a class="reference internal" href="#query-syntax" id="id91">Query Syntax</a></p>
 <ul>
-<li><p><a class="reference internal" href="#basic-query-syntax" id="id87">Basic Query Syntax</a></p>
+<li><p><a class="reference internal" href="#basic-query-syntax" id="id92">Basic Query Syntax</a></p>
 <ul>
-<li><p><a class="reference internal" href="#conditional-pruning" id="id88">Conditional pruning</a></p></li>
-<li><p><a class="reference internal" href="#conditional-highlight" id="id89">Conditional highlight</a></p></li>
+<li><p><a class="reference internal" href="#conditional-pruning" id="id93">Conditional pruning</a></p></li>
+<li><p><a class="reference internal" href="#conditional-highlight" id="id94">Conditional highlight</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#query-in-internal-nodes" id="id90">Query in internal nodes</a></p></li>
-<li><p><a class="reference internal" href="#and-and-or-conditions" id="id91">AND and OR conditions</a></p></li>
+<li><p><a class="reference internal" href="#query-in-internal-nodes" id="id95">Query in internal nodes</a></p></li>
+<li><p><a class="reference internal" href="#and-and-or-conditions" id="id96">AND and OR conditions</a></p></li>
+<li><p><a class="reference internal" href="#conditional-query-with-config-file" id="id97">Conditional query with config file</a></p>
+<ul>
+<li><p><a class="reference internal" href="#highlight-with-custom-config" id="id98">Highlight with custom config</a></p></li>
+<li><p><a class="reference internal" href="#collapse-with-custom-config" id="id99">Collapse with custom config</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#conditional-limit-based-on-taxonomic-level" id="id92">Conditional limit based on taxonomic level</a></p></li>
-<li><p><a class="reference internal" href="#choose-the-metric-for-internal-nodes-in-numerical-layout" id="id93">Choose the metric for internal nodes in numerical layout</a></p></li>
 </ul>
 </li>
-<li><p><a class="reference internal" href="#demo1-explore-gtdb-taxonomic-tree-with-metadata-and-habitat-information-of-progenome3" id="id94">Demo1 Explore GTDB taxonomic tree with metadata and habitat information of progenome3</a></p></li>
-<li><p><a class="reference internal" href="#demo2-explore-large-nifh-gene-tree-with-functional-and-taxonomic-information" id="id95">Demo2 Explore large NifH gene tree with functional and taxonomic information</a></p></li>
+<li><p><a class="reference internal" href="#conditional-limit-based-on-taxonomic-level" id="id100">Conditional limit based on taxonomic level</a></p></li>
+<li><p><a class="reference internal" href="#choose-the-metric-for-internal-nodes-in-numerical-layout" id="id101">Choose the metric for internal nodes in numerical layout</a></p></li>
+</ul>
+</li>
+<li><p><a class="reference internal" href="#demo1-explore-gtdb-taxonomic-tree-with-metadata-and-habitat-information-of-progenome3" id="id102">Demo1 Explore GTDB taxonomic tree with metadata and habitat information of progenome3</a></p></li>
+<li><p><a class="reference internal" href="#demo2-explore-large-nifh-gene-tree-with-functional-and-taxonomic-information" id="id103">Demo2 Explore large NifH gene tree with functional and taxonomic information</a></p></li>
 </ul>
 </li>
 </ul>
 </nav>
 </section>
 <section id="installation">
-<h1><a class="toc-backref" href="#id6" role="doc-backlink">Installation</a><a class="headerlink" href="#installation" title="Link to this heading">¶</a></h1>
+<h1><a class="toc-backref" href="#id7" role="doc-backlink">Installation</a><a class="headerlink" href="#installation" title="Link to this heading">¶</a></h1>
 <section id="dependencies">
-<h2><a class="toc-backref" href="#id7" role="doc-backlink">Dependencies</a><a class="headerlink" href="#dependencies" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id8" role="doc-backlink">Dependencies</a><a class="headerlink" href="#dependencies" title="Link to this heading">¶</a></h2>
 <dl class="simple">
 <dt>TreeProfiler requires</dt><dd><ul class="simple">
-<li><p>Python version &gt;= 3.9</p></li>
+<li><p>Python version &gt;= 3.10</p></li>
 <li><p>ETE Toolkit v4</p></li>
-<li><p>biopython</p></li>
-<li><p>selenium</p></li>
-<li><p>scipy</p></li>
-<li><p>matplotlib</p></li>
-<li><p>numba</p></li>
+<li><p>biopython &gt;= 1.8</p></li>
+<li><p>selenium &gt;= 4.24</p></li>
+<li><p>scipy &gt;= 1.8.0</p></li>
+<li><p>matplotlib &gt;= 3.4</p></li>
+<li><p>pymc &gt;= 5.0.0</p></li>
+<li><p>aesara</p></li>
 <li><p>pastml (custom)</p></li>
 </ul>
 </dd>
 </dl>
 </section>
 <section id="quick-install-via-pip">
-<h2><a class="toc-backref" href="#id8" role="doc-backlink">Quick install via pip</a><a class="headerlink" href="#quick-install-via-pip" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id9" role="doc-backlink">Quick install via pip</a><a class="headerlink" href="#quick-install-via-pip" title="Link to this heading">¶</a></h2>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># Install ETE Toolkit v4</span>
 <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">force</span><span class="o">-</span><span class="n">reinstall</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">etetoolkit</span><span class="o">/</span><span class="n">ete</span><span class="o">/</span><span class="n">archive</span><span class="o">/</span><span class="n">ete4</span><span class="o">.</span><span class="n">zip</span>
 
+
 <span class="c1"># Install TreeProfiler dependencies</span>
-<span class="n">pip</span> <span class="n">install</span> <span class="n">biopython</span> <span class="n">selenium</span> <span class="n">scipy</span> <span class="n">matplotlib</span> <span class="n">numba</span>
+<span class="n">pip</span> <span class="n">install</span> <span class="n">biopython</span> <span class="n">selenium</span> <span class="n">scipy</span> <span class="n">matplotlib</span> <span class="n">pymc</span> <span class="n">aesara</span>
 
 <span class="c1"># Install custom pastml package for ete4</span>
 <span class="n">pip</span> <span class="n">install</span> <span class="s2">&quot;git+https://github.com/dengzq1234/pastml.git@pastml2ete4&quot;</span>
@@ -237,7 +253,7 @@ <h2><a class="toc-backref" href="#id8" role="doc-backlink">Quick install via pip
 <span class="c1"># Install TreeProfiler tool via pip</span>
 <span class="n">pip</span> <span class="n">install</span> <span class="n">TreeProfiler</span>
 
-<span class="c1"># or installing main repo</span>
+<span class="c1"># Or install directly from github</span>
 <span class="n">pip</span> <span class="n">install</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">compgenomicslab</span><span class="o">/</span><span class="n">TreeProfiler</span><span class="o">/</span><span class="n">archive</span><span class="o">/</span><span class="n">main</span><span class="o">.</span><span class="n">zip</span>
 <span class="c1"># or development mode for latestest update</span>
 <span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">compgenomicslab</span><span class="o">/</span><span class="n">TreeProfiler</span><span class="nd">@dev</span><span class="o">-</span><span class="n">repo</span>
@@ -245,7 +261,7 @@ <h2><a class="toc-backref" href="#id8" role="doc-backlink">Quick install via pip
 </div>
 </section>
 <section id="quick-start-with-examples-dataset">
-<h2><a class="toc-backref" href="#id9" role="doc-backlink">Quick Start with examples dataset</a><a class="headerlink" href="#quick-start-with-examples-dataset" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id10" role="doc-backlink">Quick Start with examples dataset</a><a class="headerlink" href="#quick-start-with-examples-dataset" title="Link to this heading">¶</a></h2>
 <p>TreeProfiler provide various example dataset for testing in <code class="docutils literal notranslate"><span class="pre">examples/</span></code> or <a class="reference external" href="https://github.com/compgenomicslab/TreeProfiler/tree/main/examples">https://github.com/compgenomicslab/TreeProfiler/tree/main/examples</a>, each directory consists a demo script <code class="docutils literal notranslate"><span class="pre">*_demo.sh</span></code> for quick starting different functions in TreeProfiler which already has annotate-plot pipeline of example data. User can fast explore different example tree with different visualizations. Here is the demonstration:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># execute demo script of example1</span>
 <span class="n">cd</span> <span class="n">examples</span><span class="o">/</span><span class="n">basic_example1</span><span class="o">/</span>
@@ -291,9 +307,9 @@ <h2><a class="toc-backref" href="#id9" role="doc-backlink">Quick Start with exam
 </div>
 </section>
 <section id="manual-installation">
-<h2><a class="toc-backref" href="#id10" role="doc-backlink">Manual installation</a><a class="headerlink" href="#manual-installation" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id11" role="doc-backlink">Manual installation</a><a class="headerlink" href="#manual-installation" title="Link to this heading">¶</a></h2>
 <section id="install-ete-v4">
-<h3><a class="toc-backref" href="#id11" role="doc-backlink">Install ETE v4</a><a class="headerlink" href="#install-ete-v4" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id12" role="doc-backlink">Install ETE v4</a><a class="headerlink" href="#install-ete-v4" title="Link to this heading">¶</a></h3>
 <p>Quick way</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">etetoolkit</span><span class="o">/</span><span class="n">ete</span><span class="o">/</span><span class="n">archive</span><span class="o">/</span><span class="n">ete4</span><span class="o">.</span><span class="n">zip</span>
 </pre></div>
@@ -304,7 +320,7 @@ <h3><a class="toc-backref" href="#id11" role="doc-backlink">Install ETE v4</a><a
 <li><p>Clone this repository (git clone <a class="reference external" href="https://github.com/etetoolkit/ete.git">https://github.com/etetoolkit/ete.git</a>)</p></li>
 <li><p>Install dependecies
 - If you are using conda:</p>
-<p><code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">install</span> <span class="pre">-c</span> <span class="pre">conda-forge</span> <span class="pre">cython</span> <span class="pre">bottle</span> <span class="pre">brotli</span> <span class="pre">numpy</span> <span class="pre">pyqt</span></code></p>
+<p><code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">install</span> <span class="pre">-c</span> <span class="pre">conda-forge</span> <span class="pre">cython</span> <span class="pre">bottle</span> <span class="pre">brotli</span> <span class="pre">pyqt</span> <span class="pre">numpy&lt;2.0</span></code></p>
 <ul class="simple">
 <li><p>Otherwise, you can install them with</p></li>
 </ul>
@@ -318,10 +334,10 @@ <h3><a class="toc-backref" href="#id11" role="doc-backlink">Install ETE v4</a><a
 <p>(In Linux there may be some cases where the gcc library must be installed, which can be done with <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">install</span> <span class="pre">-c</span> <span class="pre">conda-forge</span> <span class="pre">gcc_linux-64</span></code>)</p>
 </section>
 <section id="install-treeprofiler">
-<h3><a class="toc-backref" href="#id12" role="doc-backlink">Install TreeProfiler</a><a class="headerlink" href="#install-treeprofiler" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id13" role="doc-backlink">Install TreeProfiler</a><a class="headerlink" href="#install-treeprofiler" title="Link to this heading">¶</a></h3>
 <p>Install dependencies</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># install BioPython, selenium, scipy via conda</span>
-<span class="n">conda</span> <span class="n">install</span> <span class="o">-</span><span class="n">c</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span> <span class="n">biopython</span> <span class="n">selenium</span> <span class="n">scipy</span> <span class="n">matplotlib</span>
+<span class="n">conda</span> <span class="n">install</span> <span class="o">-</span><span class="n">c</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span> <span class="n">biopython</span> <span class="n">selenium</span> <span class="n">scipy</span> <span class="n">matplotlib</span> <span class="n">pymc</span>
 
 <span class="c1"># or pip</span>
 <span class="n">pip</span> <span class="n">install</span> <span class="n">biopython</span> <span class="n">selenium</span> <span class="n">scipy</span> <span class="n">matplotlib</span>
@@ -336,13 +352,13 @@ <h3><a class="toc-backref" href="#id12" role="doc-backlink">Install TreeProfiler
 </div>
 <p>or install inrectly from github</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># install directly</span>
-<span class="n">pip</span> <span class="n">install</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">dengzq1234</span><span class="o">/</span><span class="n">TreeProfiler</span><span class="o">/</span><span class="n">archive</span><span class="o">/</span><span class="n">refs</span><span class="o">/</span><span class="n">tags</span><span class="o">/</span><span class="n">v1</span><span class="mf">.1.0</span><span class="o">.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
+<span class="n">pip</span> <span class="n">install</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">compgenomicslab</span><span class="o">/</span><span class="n">TreeProfiler</span><span class="o">/</span><span class="n">archive</span><span class="o">/</span><span class="n">main</span><span class="o">.</span><span class="n">zip</span>
 </pre></div>
 </div>
 </section>
 </section>
 <section id="input-files">
-<h2><a class="toc-backref" href="#id13" role="doc-backlink">Input files</a><a class="headerlink" href="#input-files" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id14" role="doc-backlink">Input files</a><a class="headerlink" href="#input-files" title="Link to this heading">¶</a></h2>
 <p>TreeProfiler takes following file types as input</p>
 <table class="docutils align-default">
 <thead>
@@ -365,7 +381,7 @@ <h2><a class="toc-backref" href="#id13" role="doc-backlink">Input files</a><a cl
 </ul>
 </section>
 <section id="basic-usage">
-<h2><a class="toc-backref" href="#id14" role="doc-backlink">Basic Usage</a><a class="headerlink" href="#basic-usage" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id15" role="doc-backlink">Basic Usage</a><a class="headerlink" href="#basic-usage" title="Link to this heading">¶</a></h2>
 <dl class="simple">
 <dt>TreeProfiler has two main subcommand:</dt><dd><ul class="simple">
 <li><p>annotate</p></li>
@@ -388,67 +404,12 @@ <h2><a class="toc-backref" href="#id14" role="doc-backlink">Basic Usage</a><a cl
 </section>
 </section>
 <section id="using-treeprofiler">
-<h1><a class="toc-backref" href="#id15" role="doc-backlink">Using TreeProfiler</a><a class="headerlink" href="#using-treeprofiler" title="Link to this heading">¶</a></h1>
+<h1><a class="toc-backref" href="#id16" role="doc-backlink">Using TreeProfiler</a><a class="headerlink" href="#using-treeprofiler" title="Link to this heading">¶</a></h1>
 <p>In this Tutorial we will use TreeProfiler and demostrate basic usage with data in <code class="docutils literal notranslate"><span class="pre">examples/</span></code></p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>tree examples/
-examples/
-├── automatic_query
-│   ├── basic_example1_metadata1.tsv
-│   ├── basic_example1.nw
-│   ├── collapse_demo.sh
-│   ├── highlight_demo.sh
-│   └── prune_demo.sh
-├── basic_example1
-│   ├── basic_example1_metadata1.tsv
-│   ├── basic_example1_metadata2.tsv
-│   ├── basic_example1.nw
-│   └── example1_demo.sh
-├── basic_example2
-│   ├── diauxic.array
-│   ├── diauxic.nw
-│   ├── example2_demo.sh
-│   ├── FluA_H3_AA.fas
-│   ├── MCC_FluA_H3_Genotype.txt
-│   └── MCC_FluA_H3.nw
-├── pratical_example
-│   ├── emapper
-│   │   ├── 7955.ENSDARP00000116736.aln.faa
-│   │   ├── 7955.ENSDARP00000116736.nw
-│   │   ├── 7955.out.emapper.annotations
-│   │   ├── 7955.out.emapper.pfam
-│   │   ├── 7955.out.emapper.smart.out
-│   │   ├── emapper_demo.sh
-│   │   ├── nifH.faa.aln
-│   │   ├── nifH.nw
-│   │   ├── nifH.out.emapper.annotations
-│   │   └── nifH.out.emapper.pfam
-│   ├── gtdb_r202
-│   │   ├── ar122_metadata_r202_lite.tar.gz
-│   │   ├── bac120_metadata_r202_lite.tar.gz
-│   │   ├── gtdbv202full_demo.sh
-│   │   ├── gtdbv202lite_demo.sh
-│   │   ├── gtdbv202.nw
-│   │   ├── merge_gtdbtree.py
-│   │   └── progenome3.tar.gz
-│   └── progenome3
-│       ├── progenome3.nw
-│       ├── progenome3.tsv
-│       └── progenome_demo.sh
-└── taxonomy_example
-    ├── gtdb
-    │   ├── gtdb_demo.sh
-    │   ├── gtdb_example1.nw
-    │   └── gtdb_example1.tsv
-    └── ncbi
-        ├── ncbi_demo.sh
-        ├── ncbi_example.nw
-        └── ncbi_example.tsv
-</pre></div>
-</div>
 <section id="reading-input-tree">
-<h2><a class="toc-backref" href="#id16" role="doc-backlink">Reading input tree</a><a class="headerlink" href="#reading-input-tree" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id17" role="doc-backlink">Reading input tree</a><a class="headerlink" href="#reading-input-tree" title="Link to this heading">¶</a></h2>
 <section id="tree-format">
-<h3><a class="toc-backref" href="#id17" role="doc-backlink">Tree format</a><a class="headerlink" href="#tree-format" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id18" role="doc-backlink">Tree format</a><a class="headerlink" href="#tree-format" title="Link to this heading">¶</a></h3>
 <p>TreeProfiler accpept input tree in <code class="docutils literal notranslate"><span class="pre">.nw</span></code> or <code class="docutils literal notranslate"><span class="pre">.ete</span></code> by putting <code class="docutils literal notranslate"><span class="pre">--input-type</span> <span class="pre">{newick,ete}</span></code> flag to identify. By default, TreeProfiler will automatically detech the format of tree. The difference between <code class="docutils literal notranslate"><span class="pre">.nw</span></code> and <code class="docutils literal notranslate"><span class="pre">.ete</span></code>:</p>
 <blockquote>
 <div><ul class="simple">
@@ -458,7 +419,7 @@ <h3><a class="toc-backref" href="#id17" role="doc-backlink">Tree format</a><a cl
 </div></blockquote>
 </section>
 <section id="tree-parser">
-<h3><a class="toc-backref" href="#id18" role="doc-backlink">Tree parser</a><a class="headerlink" href="#tree-parser" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id19" role="doc-backlink">Tree parser</a><a class="headerlink" href="#tree-parser" title="Link to this heading">¶</a></h3>
 <p>TreeProfiler provides argument <code class="docutils literal notranslate"><span class="pre">--internal</span> <span class="pre">{name,support}</span></code> to specify <code class="docutils literal notranslate"><span class="pre">newick</span></code> tree when it include values in internal node. <code class="docutils literal notranslate"><span class="pre">[default:</span> <span class="pre">name]</span></code></p>
 <table class="docutils align-default">
 <thead>
@@ -484,7 +445,7 @@ <h3><a class="toc-backref" href="#id18" role="doc-backlink">Tree parser</a><a cl
 </section>
 </section>
 <section id="treeprofiler-annotate-computing-phylogenetic-profiles-and-annotation">
-<h2><a class="toc-backref" href="#id19" role="doc-backlink"><code class="docutils literal notranslate"><span class="pre">treeprofiler-annotate</span></code> computing phylogenetic profiles and annotation</a><a class="headerlink" href="#treeprofiler-annotate-computing-phylogenetic-profiles-and-annotation" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id20" role="doc-backlink"><code class="docutils literal notranslate"><span class="pre">treeprofiler-annotate</span></code> computing phylogenetic profiles and annotation</a><a class="headerlink" href="#treeprofiler-annotate-computing-phylogenetic-profiles-and-annotation" title="Link to this heading">¶</a></h2>
 <p>TreeProfiler <code class="docutils literal notranslate"><span class="pre">annotate</span></code> subcommand is the step that annotate input metadata to target tree. As a result, itwill generate the following output file:</p>
 <ol class="arabic simple">
 <li><p><code class="docutils literal notranslate"><span class="pre">&lt;input_tree&gt;</span></code> + <em>_annotated.nw</em>, newick format with annotated tree</p></li>
@@ -493,7 +454,7 @@ <h2><a class="toc-backref" href="#id19" role="doc-backlink"><code class="docutil
 <li><p><code class="docutils literal notranslate"><span class="pre">&lt;input_tree&gt;</span></code> + <em>_annotated.tsv</em>,  metadata in tab-sarated values format with annotated and summarized internal nodes information.</p></li>
 </ol>
 <section id="annotate-metadata-into-tree">
-<h3><a class="toc-backref" href="#id20" role="doc-backlink">Annotate metadata into tree</a><a class="headerlink" href="#annotate-metadata-into-tree" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id21" role="doc-backlink">Annotate metadata into tree</a><a class="headerlink" href="#annotate-metadata-into-tree" title="Link to this heading">¶</a></h3>
 <p>In the following sub session we will describe the usage of following arguments in <code class="docutils literal notranslate"><span class="pre">annotate</span></code> step for metadata:</p>
 <table class="docutils align-default">
 <thead>
@@ -520,7 +481,7 @@ <h3><a class="toc-backref" href="#id20" role="doc-backlink">Annotate metadata in
 </tbody>
 </table>
 <section id="basic-metadata-in-tsv-csv-format">
-<h4><a class="toc-backref" href="#id21" role="doc-backlink">Basic metadata in TSV/CSV format</a><a class="headerlink" href="#basic-metadata-in-tsv-csv-format" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id22" role="doc-backlink">Basic metadata in TSV/CSV format</a><a class="headerlink" href="#basic-metadata-in-tsv-csv-format" title="Link to this heading">¶</a></h4>
 <p>TreeProfiler allows users to input metadata in tsv/csv file by setting <code class="docutils literal notranslate"><span class="pre">--metadata</span> <span class="pre">&lt;filename.tsv|.csv&gt;</span></code>  and <code class="docutils literal notranslate"><span class="pre">-s</span> <span class="pre">&lt;seperator&gt;</span></code>. By default, the first column of metadata should be names of target tree leaves and metadata should contain column names for each column of metadata.</p>
 <p>For annotating more than one metadata inputs to tree such as <code class="docutils literal notranslate"><span class="pre">--metadata</span> <span class="pre">table1.tsv</span> <span class="pre">table2.tsv</span></code>.</p>
 <p>Check metadata</p>
@@ -571,7 +532,7 @@ <h4><a class="toc-backref" href="#id21" role="doc-backlink">Basic metadata in TS
 </div>
 </section>
 <section id="metadata-tsv-csv-as-a-numerical-data-matrix">
-<h4><a class="toc-backref" href="#id22" role="doc-backlink">Metadata TSV/CSV as a numerical data matrix</a><a class="headerlink" href="#metadata-tsv-csv-as-a-numerical-data-matrix" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id23" role="doc-backlink">Metadata TSV/CSV as a numerical data matrix</a><a class="headerlink" href="#metadata-tsv-csv-as-a-numerical-data-matrix" title="Link to this heading">¶</a></h4>
 <p>treeprofiler can handle the whole tsv/csv file as one property and annotate it to related leaves, by using <code class="docutils literal notranslate"><span class="pre">--data-matrix</span> <span class="pre">&lt;filename.tsv|.csv&gt;</span></code> It must be numerical data matrix and without headers. Once annotated the property of data-matrix will be named by the filename (see example below)</p>
 <p>The difference between <code class="docutils literal notranslate"><span class="pre">--data-matrix</span></code> and <code class="docutils literal notranslate"><span class="pre">--metadata</span></code> is that the former sees the whole metadata file as a node property and stores the rows as an array in leaf nodes, and the latter sees each column from metadata as each single property of leaf nodes.</p>
 <p>Using data array file <code class="docutils literal notranslate"><span class="pre">data.array</span></code> from the previous example</p>
@@ -603,7 +564,7 @@ <h4><a class="toc-backref" href="#id22" role="doc-backlink">Metadata TSV/CSV as
 </div>
 </section>
 <section id="metadata-without-column-names">
-<h4><a class="toc-backref" href="#id23" role="doc-backlink">Metadata without column names</a><a class="headerlink" href="#metadata-without-column-names" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id24" role="doc-backlink">Metadata without column names</a><a class="headerlink" href="#metadata-without-column-names" title="Link to this heading">¶</a></h4>
 <p>If metadata does not have headers, by setting <code class="docutils literal notranslate"><span class="pre">--no-headers</span></code> to set the metadata properly, therefore treeprofiler will name each column by <code class="docutils literal notranslate"><span class="pre">col</span></code> + <code class="docutils literal notranslate"><span class="pre">&lt;column</span> <span class="pre">number&gt;</span></code> as the property key in each leaf node, such as <code class="docutils literal notranslate"><span class="pre">col1</span></code>, <code class="docutils literal notranslate"><span class="pre">col2</span></code>, etc.</p>
 <p>Example:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># data.array doesn&#39;t have headers for each column</span>
@@ -644,7 +605,7 @@ <h4><a class="toc-backref" href="#id23" role="doc-backlink">Metadata without col
 </div>
 </section>
 <section id="missing-value-detection">
-<h4><a class="toc-backref" href="#id24" role="doc-backlink">Missing value detection</a><a class="headerlink" href="#missing-value-detection" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id25" role="doc-backlink">Missing value detection</a><a class="headerlink" href="#missing-value-detection" title="Link to this heading">¶</a></h4>
 <p>Metadata column which fullfills one of the following criterias will be consider as missing value:</p>
 <ul class="simple">
 <li><p>Entirely symbolic characters. Such as <code class="docutils literal notranslate"><span class="pre">+</span></code>, <code class="docutils literal notranslate"><span class="pre">-</span></code>, <code class="docutils literal notranslate"><span class="pre">~</span></code>, <code class="docutils literal notranslate"><span class="pre">.</span></code>, etc.</p></li>
@@ -654,11 +615,11 @@ <h4><a class="toc-backref" href="#id24" role="doc-backlink">Missing value detect
 <p>Missing value will replaced by string ‘NaN’ in the corresponding property.</p>
 </section>
 <section id="unmapped-tree-leaf-property-detection">
-<h4><a class="toc-backref" href="#id25" role="doc-backlink">Unmapped tree leaf property detection</a><a class="headerlink" href="#unmapped-tree-leaf-property-detection" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id26" role="doc-backlink">Unmapped tree leaf property detection</a><a class="headerlink" href="#unmapped-tree-leaf-property-detection" title="Link to this heading">¶</a></h4>
 <p>If Metadata doesn’t cover input tree leaf, tree leaf will be unannotated.</p>
 </section>
 <section id="handling-duplicated-leaf-names-in-metadata">
-<h4><a class="toc-backref" href="#id26" role="doc-backlink">Handling duplicated leaf names in metadata</a><a class="headerlink" href="#handling-duplicated-leaf-names-in-metadata" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id27" role="doc-backlink">Handling duplicated leaf names in metadata</a><a class="headerlink" href="#handling-duplicated-leaf-names-in-metadata" title="Link to this heading">¶</a></h4>
 <p>In general, treeprofiler expects each row of metadata corresponding to one leaf, such as</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">head</span> <span class="n">categorical</span><span class="o">.</span><span class="n">tsv</span>
 <span class="c1">#name,categorical1</span>
@@ -700,7 +661,7 @@ <h4><a class="toc-backref" href="#id26" role="doc-backlink">Handling duplicated
 </div>
 </section>
 <section id="specifying-data-types-for-metadata-columns">
-<h4><a class="toc-backref" href="#id27" role="doc-backlink">Specifying data types for metadata columns</a><a class="headerlink" href="#specifying-data-types-for-metadata-columns" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id28" role="doc-backlink">Specifying data types for metadata columns</a><a class="headerlink" href="#specifying-data-types-for-metadata-columns" title="Link to this heading">¶</a></h4>
 <p>Although TreeProfiler can automatically detect datatype of each column, users still can determine the datatype using the following arguments using:</p>
 <table class="docutils align-default">
 <thead>
@@ -734,7 +695,7 @@ <h4><a class="toc-backref" href="#id27" role="doc-backlink">Specifying data type
 </table>
 </section>
 <section id="annotate-metadata-to-internal-nodes">
-<h4><a class="toc-backref" href="#id28" role="doc-backlink">Annotate metadata to internal nodes</a><a class="headerlink" href="#annotate-metadata-to-internal-nodes" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id29" role="doc-backlink">Annotate metadata to internal nodes</a><a class="headerlink" href="#annotate-metadata-to-internal-nodes" title="Link to this heading">¶</a></h4>
 <p>At the above example, we only mapped metadata to leaf nodes, in this example, we will also profile <strong>internal nodes</strong> annotation and analysis of their children nodes. Argument that in related to summary methods are:</p>
 <table class="docutils align-default">
 <thead>
@@ -1107,12 +1068,11 @@ <h4><a class="toc-backref" href="#id28" role="doc-backlink">Annotate metadata to
 </pre></div>
 </div>
 <section id="customizing-summary-methods-for-different-columns">
-<h5><a class="toc-backref" href="#id29" role="doc-backlink">Customizing summary methods for different columns</a><a class="headerlink" href="#customizing-summary-methods-for-different-columns" title="Link to this heading">¶</a></h5>
+<h5><a class="toc-backref" href="#id30" role="doc-backlink">Customizing summary methods for different columns</a><a class="headerlink" href="#customizing-summary-methods-for-different-columns" title="Link to this heading">¶</a></h5>
 <p>Using <code class="docutils literal notranslate"><span class="pre">--column-summary-method</span></code>  can specify the summary method of each properties, simply add <code class="docutils literal notranslate"><span class="pre">&lt;property</span> <span class="pre">name&gt;=&lt;summary</span> <span class="pre">method&gt;</span></code> . For categorical data, options are <code class="docutils literal notranslate"><span class="pre">{raw,relative,none}</span></code>; for numerical data, options are  <code class="docutils literal notranslate"><span class="pre">{all,</span> <span class="pre">sum,</span> <span class="pre">avg,</span> <span class="pre">max,</span> <span class="pre">min,</span> <span class="pre">std,</span> <span class="pre">none}</span></code> .</p>
 <p>such as <code class="docutils literal notranslate"><span class="pre">--column-summary-method</span> <span class="pre">sample1=none</span> <span class="pre">sample2=avg</span> <span class="pre">random_type=relative</span> <span class="pre">alignment=none</span></code></p>
-<p>Noted that <code class="docutils literal notranslate"><span class="pre">--data-matrix</span></code> can be effected by <code class="docutils literal notranslate"><span class="pre">--column-summary-method</span> <span class="pre">``</span> <span class="pre">setting,</span> <span class="pre">in</span> <span class="pre">this</span> <span class="pre">case</span> <span class="pre">filename</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">data</span> <span class="pre">matrix</span> <span class="pre">is</span> <span class="pre">property</span> <span class="pre">name,</span> <span class="pre">such</span> <span class="pre">as</span> <span class="pre">``--data-matrix</span> <span class="pre">file.tsv</span> <span class="pre">--column-summary-method</span> <span class="pre">file.tsv=avg</span></code></p>
-<p>example:
-here we use three different metadata: <code class="docutils literal notranslate"><span class="pre">categorical.tsv</span></code>, <code class="docutils literal notranslate"><span class="pre">numerical.tsv</span></code> and <code class="docutils literal notranslate"><span class="pre">data</span> <span class="pre">matrix</span></code></p>
+<p>Noted that <code class="docutils literal notranslate"><span class="pre">--data-matrix</span></code> can be effected by <code class="docutils literal notranslate"><span class="pre">--column-summary-method</span></code> setting, in this case filename of the data matrix is property name, such as <code class="docutils literal notranslate"><span class="pre">--data-matrix</span> <span class="pre">file.tsv</span> <span class="pre">--column-summary-method</span> <span class="pre">file.tsv=avg</span></code></p>
+<p>example, here we use three different metadata: <code class="docutils literal notranslate"><span class="pre">categorical.tsv</span></code>, <code class="docutils literal notranslate"><span class="pre">numerical.tsv</span></code> and <code class="docutils literal notranslate"><span class="pre">data</span> <span class="pre">matrix</span></code></p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># cusomtize different summary methods for different column/property</span>
 <span class="n">treeprofiler</span> <span class="n">annotate</span> \
 <span class="o">-</span><span class="n">t</span> <span class="n">demo1</span><span class="o">.</span><span class="n">tree</span> \
@@ -1156,7 +1116,7 @@ <h5><a class="toc-backref" href="#id29" role="doc-backlink">Customizing summary
 </section>
 </section>
 <section id="taxonomic-annotation">
-<h3><a class="toc-backref" href="#id30" role="doc-backlink">Taxonomic annotation</a><a class="headerlink" href="#taxonomic-annotation" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id31" role="doc-backlink">Taxonomic annotation</a><a class="headerlink" href="#taxonomic-annotation" title="Link to this heading">¶</a></h3>
 <p>Treeprofiler annotate tree node with target taxonomy, you can either use [GTDB](<a class="reference external" href="https://gtdb.ecogenomic.org/">https://gtdb.ecogenomic.org/</a>) or [NCBI](<a class="reference external" href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</a>) taxonomic database, such as following commands</p>
 <table class="docutils align-default">
 <thead>
@@ -1196,7 +1156,7 @@ <h3><a class="toc-backref" href="#id30" role="doc-backlink">Taxonomic annotation
 </pre></div>
 </div>
 <section id="using-different-taxonomic-databases-from-gtdb-ncbi">
-<h4><a class="toc-backref" href="#id31" role="doc-backlink">Using different taxonomic databases from GTDB/NCBI</a><a class="headerlink" href="#using-different-taxonomic-databases-from-gtdb-ncbi" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id32" role="doc-backlink">Using different taxonomic databases from GTDB/NCBI</a><a class="headerlink" href="#using-different-taxonomic-databases-from-gtdb-ncbi" title="Link to this heading">¶</a></h4>
 <p>To start taxonomic annotation, using <code class="docutils literal notranslate"><span class="pre">--taxon-column</span></code> and <code class="docutils literal notranslate"><span class="pre">--taxadb</span></code> to locate where is the taxon and which taxonomic databases to be used. If taxon is leaf name, then using <code class="docutils literal notranslate"><span class="pre">--taxon-column</span> <span class="pre">name</span></code>. Otherwise <code class="docutils literal notranslate"><span class="pre">--taxon-column</span> <span class="pre">&lt;prop_name&gt;</span></code> which refers to the column in the metadata.</p>
 <p>Examples in NCBI taxonomic database</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># check example tree</span>
@@ -1315,37 +1275,48 @@ <h4><a class="toc-backref" href="#id31" role="doc-backlink">Using different taxo
 </div>
 </section>
 <section id="identifying-taxon-names-in-different-metadata-fields-columns">
-<h4><a class="toc-backref" href="#id32" role="doc-backlink">Identifying taxon names in different metadata fields/columns</a><a class="headerlink" href="#identifying-taxon-names-in-different-metadata-fields-columns" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id33" role="doc-backlink">Identifying taxon names in different metadata fields/columns</a><a class="headerlink" href="#identifying-taxon-names-in-different-metadata-fields-columns" title="Link to this heading">¶</a></h4>
 <p>When Taxon properties are embeded in different column or field in metadata, treeprofiler provides <code class="docutils literal notranslate"><span class="pre">--taxon-column</span></code>, <code class="docutils literal notranslate"><span class="pre">--taxon-delimiter</span></code> and <code class="docutils literal notranslate"><span class="pre">--taxa-field</span></code> to identify taxon term in order to process taxonomic annotation sucessfully. Here is summary of different cases with corresponding setting.</p>
 <table class="docutils align-default">
 <thead>
-<tr class="row-odd"><th class="head"><p>metadata</p></th>
+<tr class="row-odd"><th class="head"><p>metadata (<cite>,</cite> as column seperator)</p></th>
 <th class="head"><p>taxon to be identified</p></th>
 <th class="head"><p>command line setting</p></th>
 </tr>
 </thead>
 <tbody>
-<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname</span> <span class="pre">col1\n9598</span> <span class="pre">wt</span></code></p></td>
+<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname,col1</span></code>
+<code class="docutils literal notranslate"><span class="pre">9598,wt</span></code></p></td>
 <td><p>9598</p></td>
-<td><p><code class="docutils literal notranslate"><span class="pre">default</span></code></p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">--taxon-column</span> <span class="pre">name</span></code></p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname</span> <span class="pre">col1\n7739.XP_002609184.1</span> <span class="pre">wt</span></code></p></td>
+<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname,col1</span></code></p>
+<p><code class="docutils literal notranslate"><span class="pre">7739.XP_002609184.1,wt</span></code></p>
+</td>
 <td><p>7739</p></td>
-<td><p><code class="docutils literal notranslate"><span class="pre">--taxon-column</span> <span class="pre">&lt;default&gt;</span> <span class="pre">--taxon-delimiter</span> <span class="pre">.</span> <span class="pre">--taxa-field</span> <span class="pre">0</span></code></p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">--taxon-column</span> <span class="pre">name</span> <span class="pre">--taxon-delimiter</span> <span class="pre">.</span> <span class="pre">--taxa-field</span> <span class="pre">0</span></code></p></td>
 </tr>
-<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname</span> <span class="pre">ncbi_id\nleaf_A</span> <span class="pre">7739</span></code></p></td>
+<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname,ncbi_id</span></code></p>
+<p><code class="docutils literal notranslate"><span class="pre">leaf_A,7739</span></code></p>
+</td>
 <td><p>7739</p></td>
-<td><p><code class="docutils literal notranslate"><span class="pre">--taxon-column</span> <span class="pre">ncbi_id</span> <span class="pre">--taxon-delimiter</span> <span class="pre">&lt;default&gt;</span> <span class="pre">--taxa-field</span> <span class="pre">&lt;default&gt;</span></code></p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">--taxon-column</span> <span class="pre">ncbi_id</span> <span class="pre">--taxon-delimiter</span> <span class="pre">.</span> <span class="pre">--taxa-field</span> <span class="pre">0</span></code></p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname</span> <span class="pre">ncbi_id\nleaf_A</span> <span class="pre">7739.XP_002609184.1</span></code></p></td>
+<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname,ncbi_id</span></code></p>
+<p><code class="docutils literal notranslate"><span class="pre">leaf_A,7739.XP_002609184.1</span></code></p>
+</td>
 <td><p>7739</p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">--taxon-column</span> <span class="pre">ncbi_id</span> <span class="pre">--taxon-delimiter</span> <span class="pre">.</span> <span class="pre">--taxa-field</span> <span class="pre">0</span></code></p></td>
 </tr>
-<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname</span> <span class="pre">col1\nRS_GCF_001560035.1</span> <span class="pre">wt</span></code></p></td>
+<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname,col1</span></code></p>
+<p><code class="docutils literal notranslate"><span class="pre">RS_GCF_001560035.1,wt</span></code></p>
+</td>
 <td><p>RS_GCF_001560035.1</p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">default</span></code></p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname</span> <span class="pre">gtdb_id\nleaf_A</span> <span class="pre">d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__Kariarchaeaceae;g__LC-2;s__LC-2</span> <span class="pre">sp001940725</span></code></p></td>
+<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">#leafname,gtdb_id</span></code></p>
+<p><code class="docutils literal notranslate"><span class="pre">leaf_A,d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__Kariarchaeaceae;g__LC-2;s__LC-2</span> <span class="pre">sp001940725</span></code></p>
+</td>
 <td><p>s__LC-2 sp001940725</p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">--taxon-column</span> <span class="pre">gtdb_id</span> <span class="pre">--taxon-delimiter</span> <span class="pre">;</span> <span class="pre">--taxa-field</span> <span class="pre">-1</span></code></p></td>
 </tr>
@@ -1404,7 +1375,7 @@ <h4><a class="toc-backref" href="#id32" role="doc-backlink">Identifying taxon na
 </div>
 </section>
 <section id="ignoring-unclassified-taxonomic-annotations">
-<h4><a class="toc-backref" href="#id33" role="doc-backlink">Ignoring unclassified taxonomic annotations</a><a class="headerlink" href="#ignoring-unclassified-taxonomic-annotations" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id34" role="doc-backlink">Ignoring unclassified taxonomic annotations</a><a class="headerlink" href="#ignoring-unclassified-taxonomic-annotations" title="Link to this heading">¶</a></h4>
 <p>Taxonomic annotation will annotate the internal nodes based on the taxa of leaf nodes, but if leaf node has unknown taxonomic information, the internal nodes will return unknown annotation. Using <code class="docutils literal notranslate"><span class="pre">--ignore-unclassified</span></code> to ignore the unknown annotation from leaves.</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># check tree with unknown taxa</span>
@@ -1481,11 +1452,11 @@ <h4><a class="toc-backref" href="#id33" role="doc-backlink">Ignoring unclassifie
 </section>
 </section>
 <section id="functional-annotation">
-<h3><a class="toc-backref" href="#id34" role="doc-backlink">Functional annotation</a><a class="headerlink" href="#functional-annotation" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id35" role="doc-backlink">Functional annotation</a><a class="headerlink" href="#functional-annotation" title="Link to this heading">¶</a></h3>
 <p>Treeprofiler provides module to annotate the tree leaf with functional annotation and sequence alignment file, such as eggnog-mapper output and multiple sequence alignments</p>
 <p>In the following session we use example in <code class="docutils literal notranslate"><span class="pre">examples/pratical_example/emapper</span></code></p>
 <section id="annotating-multiple-sequence-alignments-msa">
-<h4><a class="toc-backref" href="#id35" role="doc-backlink">Annotating Multiple Sequence Alignments(MSA)</a><a class="headerlink" href="#annotating-multiple-sequence-alignments-msa" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id36" role="doc-backlink">Annotating Multiple Sequence Alignments(MSA)</a><a class="headerlink" href="#annotating-multiple-sequence-alignments-msa" title="Link to this heading">¶</a></h4>
 <p>treeprofiler can anntotate msa to tree and automatically calculate the consesus sequence in the internal node (fixed threshold 0.7), alignment will stored in nodes with property name <cite>alignment</cite>. Using <cite>–column-summary-method alignment=none</cite> can switch off the function for calculating consensus sequence for internal nodes.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># annotate alignment</span>
 <span class="n">treeprofiler</span> <span class="n">annotate</span> <span class="o">--</span><span class="n">tree</span> <span class="n">nifH</span><span class="o">.</span><span class="n">nw</span> <span class="o">--</span><span class="n">alignment</span> <span class="n">nifH</span><span class="o">.</span><span class="n">faa</span><span class="o">.</span><span class="n">aln</span>
@@ -1500,7 +1471,7 @@ <h4><a class="toc-backref" href="#id35" role="doc-backlink">Annotating Multiple
 </div>
 </section>
 <section id="annotating-eggnog-mapper-output-and-domain-information">
-<h4><a class="toc-backref" href="#id36" role="doc-backlink">Annotating EggNOG-Mapper output and Domain information</a><a class="headerlink" href="#annotating-eggnog-mapper-output-and-domain-information" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id37" role="doc-backlink">Annotating EggNOG-Mapper output and Domain information</a><a class="headerlink" href="#annotating-eggnog-mapper-output-and-domain-information" title="Link to this heading">¶</a></h4>
 <p>[EggNOG-mapper](<a class="reference external" href="http://eggnog-mapper.embl.de/">http://eggnog-mapper.embl.de/</a>), is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (<a class="reference external" href="http://eggnog5.embl.de">http://eggnog5.embl.de</a>) to transfer functional information from fine-grained orthologs only.</p>
 <table class="docutils align-default">
 <thead>
@@ -1570,8 +1541,8 @@ <h4><a class="toc-backref" href="#id36" role="doc-backlink">Annotating EggNOG-Ma
 </ul>
 </dd>
 </dl>
-<table class="docutils align-default" id="id2">
-<caption><span class="caption-text">emapper annotation output and the summary method</span><a class="headerlink" href="#id2" title="Link to this table">¶</a></caption>
+<table class="docutils align-default" id="id3">
+<caption><span class="caption-text">emapper annotation output and the summary method</span><a class="headerlink" href="#id3" title="Link to this table">¶</a></caption>
 <thead>
 <tr class="row-odd"><th class="head"><p>Field</p></th>
 <th class="head"><p>datatype</p></th>
@@ -1665,10 +1636,10 @@ <h4><a class="toc-backref" href="#id36" role="doc-backlink">Annotating EggNOG-Ma
 </section>
 </section>
 <section id="analytical-methods-in-treeprofiler">
-<h3><a class="toc-backref" href="#id37" role="doc-backlink">Analytical methods in treeProfiler</a><a class="headerlink" href="#analytical-methods-in-treeprofiler" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id38" role="doc-backlink">Analytical methods in treeProfiler</a><a class="headerlink" href="#analytical-methods-in-treeprofiler" title="Link to this heading">¶</a></h3>
 <p>we use examples in <code class="docutils literal notranslate"><span class="pre">examples/analytic_example</span></code></p>
 <section id="ancestral-character-reconstruction">
-<h4><a class="toc-backref" href="#id38" role="doc-backlink">Ancestral character reconstruction</a><a class="headerlink" href="#ancestral-character-reconstruction" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id39" role="doc-backlink">Ancestral character reconstruction</a><a class="headerlink" href="#ancestral-character-reconstruction" title="Link to this heading">¶</a></h4>
 <p>treeprofiler has integrated [pastml](<a class="reference external" href="https://github.com/evolbioinfo/pastml">https://github.com/evolbioinfo/pastml</a>), a flexible platform for ancestral reconstruction with tree with –reconstruct flag in annotate step such as:</p>
 <table class="docutils align-default">
 <thead>
@@ -1680,14 +1651,24 @@ <h4><a class="toc-backref" href="#id38" role="doc-backlink">Ancestral character
 <tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--acr-discrete-columns</span> <span class="pre">ACR_DISCRETE_COLUMNS</span> <span class="pre">[ACR_DISCRETE_COLUMNS</span> <span class="pre">...]</span></code></p></td>
 <td><p>names of columns to perform acr analysis for discrete traits</p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--prediction-method</span> <span class="pre">{MPPA,MAP,JOINT,DOWNPASS,ACCTRAN,DELTRAN,COPY,ALL,ML,MP}</span></code></p></td>
-<td><p>Prediction method for ACR discrete analysis. Options: MPPA, MAP, JOINT, DOWNPASS, ACCTRAN, DELTRAN, COPY, ALL, ML, MP. <cite>[Default: MPPA]</cite></p></td>
+<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--acr-continuous-columns</span> <span class="pre">ACR_CONTINUOUS_COLUMNS</span> <span class="pre">[ACR_CONTINUOUS_COLUMNS</span> <span class="pre">...]</span></code></p></td>
+<td><p>names of columns to perform acr analysis for continuous traits</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--prediction-method</span> <span class="pre">{MPPA,MAP,JOINT,DOWNPASS,ACCTRAN,DELTRAN,COPY,ALL,MP,ML,BAYESIAN}</span></code></p></td>
+<td><p>Prediction method for ACR analysis.
+For <strong>Discrete</strong> traits: <code class="docutils literal notranslate"><span class="pre">MPPA</span></code>, <code class="docutils literal notranslate"><span class="pre">MAP</span></code>, <code class="docutils literal notranslate"><span class="pre">JOINT</span></code>, <code class="docutils literal notranslate"><span class="pre">DOWNPASS</span></code>, <code class="docutils literal notranslate"><span class="pre">ACCTRAN</span></code>, <code class="docutils literal notranslate"><span class="pre">DELTRAN</span></code>, <code class="docutils literal notranslate"><span class="pre">COPY</span></code>, <code class="docutils literal notranslate"><span class="pre">ALL</span></code>, <code class="docutils literal notranslate"><span class="pre">ML</span></code>, <code class="docutils literal notranslate"><span class="pre">MP</span></code>.
+For <strong>Continuous</strong> traits: <code class="docutils literal notranslate"><span class="pre">ML</span></code>, <code class="docutils literal notranslate"><span class="pre">BAYESIAN</span></code>.
+<code class="docutils literal notranslate"><span class="pre">[Default:</span> <span class="pre">MPPA]</span></code></p></td>
 </tr>
-<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--model</span> <span class="pre">{JC,</span> <span class="pre">F81,</span> <span class="pre">EFT,</span> <span class="pre">HKY,</span> <span class="pre">JTT}</span></code></p></td>
-<td><p>Evolutionary model for ML methods in ACR discrete analysis. Options: JC, F81, EFT, HKY, JTT. <cite>[Default: F81]</cite></p></td>
+<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--model</span> <span class="pre">{JC,F81,EFT,HKY,JTT,BM,OU}</span></code></p></td>
+<td><p>Evolutionary model for ML methods in ACR analysis.
+For <strong>discrete traits</strong>: <code class="docutils literal notranslate"><span class="pre">JC</span></code>, <code class="docutils literal notranslate"><span class="pre">F81</span></code>, <code class="docutils literal notranslate"><span class="pre">EFT</span></code>, <code class="docutils literal notranslate"><span class="pre">HKY</span></code>, <code class="docutils literal notranslate"><span class="pre">JTT</span></code>
+For <strong>continuous traits</strong>: <code class="docutils literal notranslate"><span class="pre">BM</span></code>, <code class="docutils literal notranslate"><span class="pre">OU</span></code>.
+<code class="docutils literal notranslate"><span class="pre">[Default:</span> <span class="pre">F81]</span></code></p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--threads</span> <span class="pre">THREADS</span></code></p></td>
-<td><p>Number of threads to use for annotation. <cite>[Default: 4]</cite></p></td>
+<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--threads</span> <span class="pre">THREADS</span></code></p></td>
+<td><p>Number of threads to use for annotation.
+<code class="docutils literal notranslate"><span class="pre">[Default:</span> <span class="pre">4]</span></code></p></td>
 </tr>
 </tbody>
 </table>
@@ -1864,7 +1845,7 @@ <h4><a class="toc-backref" href="#id38" role="doc-backlink">Ancestral character
 </div>
 </section>
 <section id="phylogenetic-signal-delta-statistic">
-<h4><a class="toc-backref" href="#id39" role="doc-backlink">Phylogenetic signal delta statistic</a><a class="headerlink" href="#phylogenetic-signal-delta-statistic" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id40" role="doc-backlink">Phylogenetic signal delta statistic</a><a class="headerlink" href="#phylogenetic-signal-delta-statistic" title="Link to this heading">¶</a></h4>
 <p>Running signal delta statistic required running Ancestral Character Reconstruction using MPPA or MP methods in order to have the ancestral character propabilities. Calculated delta statistic metric and p_value of given trait will be stored in root node as properties.</p>
 <table class="docutils align-default">
 <thead>
@@ -1935,8 +1916,77 @@ <h4><a class="toc-backref" href="#id39" role="doc-backlink">Phylogenetic signal
 </pre></div>
 </div>
 </section>
+<section id="acr-for-contiunous-data">
+<h4><a class="toc-backref" href="#id41" role="doc-backlink">ACR for contiunous data</a><a class="headerlink" href="#acr-for-contiunous-data" title="Link to this heading">¶</a></h4>
+<p>TreeProfiler supports ancestral character reconstruction for continuous traits using two main approaches: <strong>Maximum Likelihood (ML)</strong> and <strong>Bayesian</strong> inference. Both methods rely on evolutionary models for continuous data, specifically the <strong>Brownian Motion (BM)</strong> and <strong>Ornstein-Uhlenbeck (OU)</strong> models.</p>
+<p>TreeProfiler allows users to select the desired method and model using the following arguments:</p>
+<ul class="simple">
+<li><p><code class="docutils literal notranslate"><span class="pre">--acr-continuous-columns</span> <span class="pre">&lt;PROP&gt;</span></code>: Specify the column names for the continuous traits.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">--prediction-method</span> <span class="pre">&lt;ML/BAYESIAN&gt;</span></code>: Choose between the ML or Bayesian approach.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">--model</span> <span class="pre">&lt;BM/OU&gt;</span></code>: Choose the evolutionary model for continuous trait analysis.</p></li>
+</ul>
+<p>Here is tree with example metadata which is continuous dataset <code class="docutils literal notranslate"><span class="pre">Anolis.tre</span></code> and <code class="docutils literal notranslate"><span class="pre">svl.csv</span></code>:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">head</span> <span class="n">svl</span><span class="o">.</span><span class="n">csv</span>
+<span class="n">species</span><span class="p">,</span><span class="n">svl</span>
+<span class="n">ahli</span><span class="p">,</span><span class="mf">4.039125443</span>
+<span class="n">alayoni</span><span class="p">,</span><span class="mf">3.815704818</span>
+<span class="n">alfaroi</span><span class="p">,</span><span class="mf">3.526654599</span>
+<span class="n">aliniger</span><span class="p">,</span><span class="mf">4.036556538</span>
+<span class="n">allisoni</span><span class="p">,</span><span class="mf">4.375390078</span>
+
+<span class="c1"># now we run the acr for the continuous trait svl, here we turn off the descriptive statistic</span>
+<span class="n">treeprofiler</span> <span class="n">annotate</span> \
+<span class="o">-</span><span class="n">t</span> <span class="n">Anolis</span><span class="o">.</span><span class="n">tre</span> \
+<span class="o">--</span><span class="n">metadata</span> <span class="n">svl</span><span class="o">.</span><span class="n">csv</span> \
+<span class="o">-</span><span class="n">s</span> <span class="p">,</span> \
+<span class="o">--</span><span class="n">acr</span><span class="o">-</span><span class="n">continuous</span><span class="o">-</span><span class="n">columns</span> <span class="n">svl</span> \
+<span class="o">--</span><span class="n">prediction</span><span class="o">-</span><span class="n">method</span> <span class="n">ML</span> \
+<span class="o">--</span><span class="n">model</span> <span class="n">BM</span> \
+<span class="o">--</span><span class="n">num</span><span class="o">-</span><span class="n">stat</span> <span class="n">none</span> \
+<span class="o">-</span><span class="n">o</span> <span class="o">./</span>
+
+<span class="c1"># now we check the</span>
+<span class="n">python</span> <span class="n">show_tree_props</span><span class="o">.</span><span class="n">py</span> <span class="n">Anolis_annotated</span><span class="o">.</span><span class="n">nw</span>
+<span class="n">Target</span> <span class="n">tree</span> <span class="n">internal</span> <span class="n">node</span> <span class="n">Root</span> <span class="n">contains</span> <span class="n">the</span> <span class="n">following</span> <span class="n">properties</span><span class="p">:</span>
+<span class="p">{</span>
+  <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Root&#39;</span><span class="p">,</span>
+  <span class="s1">&#39;svl&#39;</span><span class="p">:</span> <span class="s1">&#39;4.065917563705425&#39;</span><span class="p">,</span>
+<span class="p">}</span>
+<span class="n">Target</span> <span class="n">tree</span> <span class="n">leaf</span> <span class="n">node</span> <span class="n">ahlicontains</span> <span class="n">the</span> <span class="n">following</span> <span class="n">propertiies</span><span class="p">:</span>
+<span class="p">{</span>
+  <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;ahli&#39;</span><span class="p">,</span>
+  <span class="s1">&#39;dist&#39;</span><span class="p">:</span> <span class="mf">0.130889</span><span class="p">,</span>
+  <span class="s1">&#39;svl&#39;</span><span class="p">:</span> <span class="s1">&#39;4.039125443&#39;</span>
+<span class="p">}</span>
+
+<span class="c1"># use Bayesian method with OU model</span>
+<span class="n">treeprofiler</span> <span class="n">annotate</span> \
+<span class="o">-</span><span class="n">t</span> <span class="n">Anolis</span><span class="o">.</span><span class="n">tre</span> \
+<span class="o">--</span><span class="n">metadata</span> <span class="n">svl</span><span class="o">.</span><span class="n">csv</span> \
+<span class="o">-</span><span class="n">s</span> <span class="p">,</span> \
+<span class="o">--</span><span class="n">acr</span><span class="o">-</span><span class="n">continuous</span><span class="o">-</span><span class="n">columns</span> <span class="n">svl</span> \
+<span class="o">--</span><span class="n">prediction</span><span class="o">-</span><span class="n">method</span> <span class="n">BAYESIAN</span> \
+<span class="o">--</span><span class="n">model</span> <span class="n">OU</span> \
+<span class="o">--</span><span class="n">num</span><span class="o">-</span><span class="n">stat</span> <span class="n">none</span> \
+<span class="o">-</span><span class="n">o</span> <span class="o">./</span>
+
+<span class="n">python</span> <span class="n">show_tree_props</span><span class="o">.</span><span class="n">py</span> <span class="n">Anolis_annotated</span><span class="o">.</span><span class="n">nw</span>
+<span class="n">Target</span> <span class="n">tree</span> <span class="n">internal</span> <span class="n">node</span> <span class="n">Root</span> <span class="n">contains</span> <span class="n">the</span> <span class="n">following</span> <span class="n">properties</span><span class="p">:</span>
+<span class="p">{</span>
+  <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Root&#39;</span><span class="p">,</span>
+  <span class="s1">&#39;svl&#39;</span><span class="p">:</span> <span class="s1">&#39;4.443782202699844&#39;</span>
+<span class="p">}</span>
+<span class="n">Target</span> <span class="n">tree</span> <span class="n">leaf</span> <span class="n">node</span> <span class="n">ahlicontains</span> <span class="n">the</span> <span class="n">following</span> <span class="n">propertiies</span><span class="p">:</span>
+<span class="p">{</span>
+  <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;ahli&#39;</span><span class="p">,</span>
+  <span class="s1">&#39;dist&#39;</span><span class="p">:</span> <span class="mf">0.130889</span><span class="p">,</span>
+  <span class="s1">&#39;svl&#39;</span><span class="p">:</span> <span class="s1">&#39;4.039125443&#39;</span>
+<span class="p">}</span>
+</pre></div>
+</div>
+</section>
 <section id="lineage-specificity-analysis">
-<h4><a class="toc-backref" href="#id40" role="doc-backlink">Lineage specificity analysis</a><a class="headerlink" href="#lineage-specificity-analysis" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id42" role="doc-backlink">Lineage specificity analysis</a><a class="headerlink" href="#lineage-specificity-analysis" title="Link to this heading">¶</a></h4>
 <p>Using <code class="docutils literal notranslate"><span class="pre">--ls-columns</span> <span class="pre">&lt;prop_name&gt;</span></code> to start the lineage specificity analysis of boolean traits, the given trait need to be boolean value such as <code class="docutils literal notranslate"><span class="pre">True`;</span> <span class="pre">``False</span></code>; <code class="docutils literal notranslate"><span class="pre">yes</span></code>; <code class="docutils literal notranslate"><span class="pre">no</span></code>; <code class="docutils literal notranslate"><span class="pre">t</span></code>; <code class="docutils literal notranslate"><span class="pre">f</span></code>; <code class="docutils literal notranslate"><span class="pre">1</span></code>; <code class="docutils literal notranslate"><span class="pre">0</span></code>;  which fit the criteria in treeprofiler annotate. Calculated results will be stored in each internal nodes with suffix of <code class="docutils literal notranslate"><span class="pre">_prec</span></code> , <code class="docutils literal notranslate"><span class="pre">_sens</span></code> and <code class="docutils literal notranslate"><span class="pre">_f1</span></code>.</p>
 <table class="docutils align-default">
 <thead>
@@ -1987,7 +2037,7 @@ <h4><a class="toc-backref" href="#id40" role="doc-backlink">Lineage specificity
 </section>
 </section>
 <section id="output-formats-for-annotated-trees">
-<h3><a class="toc-backref" href="#id41" role="doc-backlink">Output formats for annotated trees</a><a class="headerlink" href="#output-formats-for-annotated-trees" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id43" role="doc-backlink">Output formats for annotated trees</a><a class="headerlink" href="#output-formats-for-annotated-trees" title="Link to this heading">¶</a></h3>
 <p>TreeProfiler <code class="docutils literal notranslate"><span class="pre">annotate</span></code> subcommand will generate the following output file</p>
 <ol class="arabic simple">
 <li><p><code class="docutils literal notranslate"><span class="pre">&lt;input_tree&gt;</span></code> + <em>_annotated.nw</em>, newick format with annotated tree</p></li>
@@ -2002,16 +2052,44 @@ <h3><a class="toc-backref" href="#id41" role="doc-backlink">Output formats for a
 <li><p>ete format is a novel format developed to solve the situation we encounter in the previous step, annotated tree can be <strong>recover easily with all the annotated data without changing the data type</strong>. Besides, the ete format optimized the tree file size after mapped with its associated data. Hence it’s very handy for programers in their own script. At this moment we can only view the ete format in treeprofiler, but we will make the ete format more universal to other phylogenetic software. <strong>Hence using ete format in `plot` subcommand is highly reccomended</strong></p></li>
 </ul>
 </div></blockquote>
+<section id="use-standard-input-and-output-formats">
+<h4><a class="toc-backref" href="#id44" role="doc-backlink">Use standard input and output formats</a><a class="headerlink" href="#use-standard-input-and-output-formats" title="Link to this heading">¶</a></h4>
+<p>TreeProfiler is able to receive and produce trees in standard formats in order to integrate with command-line programs.</p>
+<ul class="simple">
+<li><p>Standard output: Use <code class="docutils literal notranslate"><span class="pre">--quiet</span></code> and <code class="docutils literal notranslate"><span class="pre">--stdout</span></code> at the same time to mute the log and output the annotated tree in Newick format.</p></li>
+</ul>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">basic_example0</span><span class="o">/</span>
+<span class="n">treeprofiler</span> <span class="n">annotate</span> \
+<span class="o">-</span><span class="n">t</span> <span class="n">demo1</span><span class="o">.</span><span class="n">tree</span> \
+<span class="o">--</span><span class="n">metadata</span> <span class="n">categorical</span><span class="o">.</span><span class="n">tsv</span> \
+<span class="o">-</span><span class="n">s</span> <span class="p">,</span> \
+<span class="o">--</span><span class="n">quiet</span> \
+<span class="o">--</span><span class="n">stdout</span>
+
+<span class="p">((</span><span class="n">Taxa_3</span><span class="p">:</span><span class="mf">0.219065</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1</span><span class="o">=</span><span class="n">C</span><span class="p">],(</span><span class="n">Taxa_4</span><span class="p">:</span><span class="mf">0.188681</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1</span><span class="o">=</span><span class="n">C</span><span class="p">],</span><span class="n">Taxa_2</span><span class="p">:</span><span class="mf">0.5196</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1</span><span class="o">=</span><span class="n">B</span><span class="p">])</span><span class="mf">0.166914</span><span class="p">:</span><span class="mf">0.90365</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1_counter</span><span class="o">=</span><span class="n">B</span><span class="o">--</span><span class="mi">1</span><span class="o">||</span><span class="n">C</span><span class="o">--</span><span class="mi">1</span><span class="p">:</span><span class="n">name</span><span class="o">=</span><span class="n">N3</span><span class="p">])</span><span class="mf">0.138062</span><span class="p">:</span><span class="mf">0.0632016</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1_counter</span><span class="o">=</span><span class="n">B</span><span class="o">--</span><span class="mi">1</span><span class="o">||</span><span class="n">C</span><span class="o">--</span><span class="mi">2</span><span class="p">:</span><span class="n">name</span><span class="o">=</span><span class="n">N4</span><span class="p">],(</span><span class="n">Taxa_0</span><span class="p">:</span><span class="mf">0.190563</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1</span><span class="o">=</span><span class="n">A</span><span class="p">],</span><span class="n">Taxa_1</span><span class="p">:</span><span class="mf">0.458423</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1</span><span class="o">=</span><span class="n">B</span><span class="p">])</span><span class="mf">0.138062</span><span class="p">:</span><span class="mf">0.97338</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1_counter</span><span class="o">=</span><span class="n">A</span><span class="o">--</span><span class="mi">1</span><span class="o">||</span><span class="n">B</span><span class="o">--</span><span class="mi">1</span><span class="p">:</span><span class="n">name</span><span class="o">=</span><span class="n">N7</span><span class="p">])[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1_counter</span><span class="o">=</span><span class="n">A</span><span class="o">--</span><span class="mi">1</span><span class="o">||</span><span class="n">B</span><span class="o">--</span><span class="mi">2</span><span class="o">||</span><span class="n">C</span><span class="o">--</span><span class="mi">2</span><span class="p">:</span><span class="n">name</span><span class="o">=</span><span class="n">Root</span><span class="p">];</span>
+</pre></div>
+</div>
+<ul class="simple">
+<li><p>Standard input, use <code class="docutils literal notranslate"><span class="pre">-</span></code> as input in <code class="docutils literal notranslate"><span class="pre">--tree</span></code> argument to take standard input into account.</p></li>
+</ul>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">basic_example0</span><span class="o">/</span>
+
+<span class="n">cat</span> <span class="n">demo1</span><span class="o">.</span><span class="n">tree</span><span class="o">|</span><span class="n">treeprofiler</span> <span class="n">annotate</span> <span class="o">-</span><span class="n">t</span> <span class="o">-</span> <span class="o">--</span><span class="n">metadata</span> <span class="n">categorical</span><span class="o">.</span><span class="n">tsv</span> <span class="o">-</span><span class="n">s</span> <span class="p">,</span> <span class="o">--</span><span class="n">quiet</span> <span class="o">--</span><span class="n">stdout</span>
+
+<span class="p">((</span><span class="n">Taxa_3</span><span class="p">:</span><span class="mf">0.219065</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1</span><span class="o">=</span><span class="n">C</span><span class="p">],(</span><span class="n">Taxa_4</span><span class="p">:</span><span class="mf">0.188681</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1</span><span class="o">=</span><span class="n">C</span><span class="p">],</span><span class="n">Taxa_2</span><span class="p">:</span><span class="mf">0.5196</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1</span><span class="o">=</span><span class="n">B</span><span class="p">])</span><span class="mf">0.166914</span><span class="p">:</span><span class="mf">0.90365</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1_counter</span><span class="o">=</span><span class="n">B</span><span class="o">--</span><span class="mi">1</span><span class="o">||</span><span class="n">C</span><span class="o">--</span><span class="mi">1</span><span class="p">:</span><span class="n">name</span><span class="o">=</span><span class="n">N3</span><span class="p">])</span><span class="mf">0.138062</span><span class="p">:</span><span class="mf">0.0632016</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1_counter</span><span class="o">=</span><span class="n">B</span><span class="o">--</span><span class="mi">1</span><span class="o">||</span><span class="n">C</span><span class="o">--</span><span class="mi">2</span><span class="p">:</span><span class="n">name</span><span class="o">=</span><span class="n">N4</span><span class="p">],(</span><span class="n">Taxa_0</span><span class="p">:</span><span class="mf">0.190563</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1</span><span class="o">=</span><span class="n">A</span><span class="p">],</span><span class="n">Taxa_1</span><span class="p">:</span><span class="mf">0.458423</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1</span><span class="o">=</span><span class="n">B</span><span class="p">])</span><span class="mf">0.138062</span><span class="p">:</span><span class="mf">0.97338</span><span class="p">[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1_counter</span><span class="o">=</span><span class="n">A</span><span class="o">--</span><span class="mi">1</span><span class="o">||</span><span class="n">B</span><span class="o">--</span><span class="mi">1</span><span class="p">:</span><span class="n">name</span><span class="o">=</span><span class="n">N7</span><span class="p">])[</span><span class="o">&amp;&amp;</span><span class="n">NHX</span><span class="p">:</span><span class="n">categorical1_counter</span><span class="o">=</span><span class="n">A</span><span class="o">--</span><span class="mi">1</span><span class="o">||</span><span class="n">B</span><span class="o">--</span><span class="mi">2</span><span class="o">||</span><span class="n">C</span><span class="o">--</span><span class="mi">2</span><span class="p">:</span><span class="n">name</span><span class="o">=</span><span class="n">Root</span><span class="p">];</span>
+</pre></div>
+</div>
+</section>
 </section>
 </section>
 <section id="treeprofiler-plot-visualizing-phylogenetic-profiles-and-annotation">
-<h2><a class="toc-backref" href="#id42" role="doc-backlink"><code class="docutils literal notranslate"><span class="pre">treeprofiler-plot</span></code> visualizing phylogenetic profiles and annotation</a><a class="headerlink" href="#treeprofiler-plot-visualizing-phylogenetic-profiles-and-annotation" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id45" role="doc-backlink"><code class="docutils literal notranslate"><span class="pre">treeprofiler-plot</span></code> visualizing phylogenetic profiles and annotation</a><a class="headerlink" href="#treeprofiler-plot-visualizing-phylogenetic-profiles-and-annotation" title="Link to this heading">¶</a></h2>
 <p>The <code class="docutils literal notranslate"><span class="pre">plot</span></code> command can be used to visually explore any annotated tree produced by the
 <code class="docutils literal notranslate"><span class="pre">annotate</span></code> program, automatically adjusting the most suitable graphical representation
 for each data source. Alternatively, users can easily adjust which annotations should be shown and
 choose among different predefined layouts.</p>
 <section id="interactive-visualization-interface">
-<h3><a class="toc-backref" href="#id43" role="doc-backlink">Interactive visualization interface</a><a class="headerlink" href="#interactive-visualization-interface" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id46" role="doc-backlink">Interactive visualization interface</a><a class="headerlink" href="#interactive-visualization-interface" title="Link to this heading">¶</a></h3>
 <p>TreeProfiler uses the new visualization framework implemented in [ETE 4.0](<a class="reference external" href="https://github.com/etetoolkit/ete/tree/ete4">https://github.com/etetoolkit/ete/tree/ete4</a>), which allows for the interactive exploration of huge phylogenies based on a context-based adaptive zooming strategy.</p>
 <p>we use example from <cite>examples/basic_example1</cite> , which contain all kind of datatype</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">head</span> <span class="o">-</span><span class="mi">3</span> <span class="n">basic_example1_metadata1</span><span class="o">.</span><span class="n">tsv</span> <span class="n">basic_example1_metadata2</span><span class="o">.</span><span class="n">tsv</span>
@@ -2045,7 +2123,7 @@ <h3><a class="toc-backref" href="#id43" role="doc-backlink">Interactive visualiz
 <p>Overview of the TreeProfiler visualization interface. (A) The control panel allows users to customize visualization layout and features, and to perform text-based searches. (B) An annotated example tree, from <code class="docutils literal notranslate"><span class="pre">examples/basic_example1/</span></code> after <code class="docutils literal notranslate"><span class="pre">annotate</span></code>, is launched with a command <code class="docutils literal notranslate"><span class="pre">plot</span></code>. Support values (red) and branch distance (grey) are displayed on top of branches. The properties of one of the nodes are shown on the top. The minimap (bottom right) facilitates navigation. (C) The node editor panel provides access to node-specific actions, such as creating subtrees, collapsing, pruning, rooting and more. (D) Visualized properties by order are, categorical data <code class="docutils literal notranslate"><span class="pre">random_type</span></code> in <code class="docutils literal notranslate"><span class="pre">rectangle-layout</span></code>, numerical data <code class="docutils literal notranslate"><span class="pre">sample1</span></code>, <code class="docutils literal notranslate"><span class="pre">sample2</span></code>, <code class="docutils literal notranslate"><span class="pre">sample3</span></code> in <code class="docutils literal notranslate"><span class="pre">heatmap-layout</span></code> and <code class="docutils literal notranslate"><span class="pre">sample4</span></code>, <code class="docutils literal notranslate"><span class="pre">sample5</span></code> in <code class="docutils literal notranslate"><span class="pre">barplot-layout</span></code>, categorical data <code class="docutils literal notranslate"><span class="pre">random_type</span></code> in <code class="docutils literal notranslate"><span class="pre">profiling-layout</span></code> shown as presence-absence matrix. Layouts are shown with the order as input argument order from the command line. Names of properties are shown as titles on the top of each layout. (E) Legends each layout is shown on the top right corner with the same order as the layouts.</p>
 </section>
 <section id="basic-options-of-visualizing-layouts">
-<h3><a class="toc-backref" href="#id44" role="doc-backlink">Basic options of visualizing layouts</a><a class="headerlink" href="#basic-options-of-visualizing-layouts" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id47" role="doc-backlink">Basic options of visualizing layouts</a><a class="headerlink" href="#basic-options-of-visualizing-layouts" title="Link to this heading">¶</a></h3>
 <p>Selected properties of tree will be visualized at the aligned panel alongside with the tree, here is some basic parameters for layouts.</p>
 <table class="docutils align-default">
 <thead>
@@ -2082,8 +2160,8 @@ <h3><a class="toc-backref" href="#id44" role="doc-backlink">Basic options of vis
 <img alt="treeprofiler interface" class="align-center" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/control_panel-0003.png?raw=true" />
 </section>
 <section id="layouts-for-categorical-data">
-<h3><a class="toc-backref" href="#id45" role="doc-backlink">Layouts for categorical data</a><a class="headerlink" href="#layouts-for-categorical-data" title="Link to this heading">¶</a></h3>
-<p>Users can add the following flag to activate layouts for categorical data</p>
+<h3><a class="toc-backref" href="#id48" role="doc-backlink">Layouts for categorical data</a><a class="headerlink" href="#layouts-for-categorical-data" title="Link to this heading">¶</a></h3>
+<p>Users can add the following flag to activate layouts for categorical data.</p>
 <table class="docutils align-default">
 <thead>
 <tr class="row-odd"><th class="head"><p>Argument</p></th>
@@ -2108,22 +2186,27 @@ <h3><a class="toc-backref" href="#id45" role="doc-backlink">Layouts for categori
 <td><p>Branch with color</p></td>
 <td><p>Stacked Horizontal RecFace (only collapsed)</p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--background-layout</span> <span class="pre">BACKGROUND_LAYOUT</span> <span class="pre">[BACKGROUND_LAYOUT</span> <span class="pre">...]</span></code></p></td>
+<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--bubble-layout</span> <span class="pre">BUBBLE_LAYOUT</span> <span class="pre">[BUBBLE_LAYOUT</span> <span class="pre">...]</span></code></p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">&lt;prop1&gt;</span> <span class="pre">&lt;prop2&gt;</span></code> names of properties where nodes will be colored based on different bubble.</p></td>
+<td><p>Circles with color</p></td>
+<td><p>None</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--background-layout</span> <span class="pre">BACKGROUND_LAYOUT</span> <span class="pre">[BACKGROUND_LAYOUT</span> <span class="pre">...]</span></code></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">&lt;prop1&gt;</span> <span class="pre">&lt;prop2&gt;</span></code> names of properties where values will be labeled as rectangular color blocks on the aligned panel.</p></td>
 <td><p>Background with color</p></td>
 <td><p>Stacked Horizontal RecFace (only collapsed)</p></td>
 </tr>
-<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--piechart-layout</span> <span class="pre">PIECHART_LAYOUT</span> <span class="pre">[PIECHART_LAYOUT</span> <span class="pre">...]</span></code></p></td>
+<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--piechart-layout</span> <span class="pre">PIECHART_LAYOUT</span> <span class="pre">[PIECHART_LAYOUT</span> <span class="pre">...]</span></code></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">&lt;prop1&gt;</span> <span class="pre">&lt;prop2&gt;</span></code> names of properties whose internal nodes need to be plotted as piechart-layout.</p></td>
 <td><p>None</p></td>
 <td><p>PiechartFace</p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--profiling-layout</span> <span class="pre">PROFILING_LAYOUT</span> <span class="pre">[PROFILING_LAYOUT</span> <span class="pre">...]</span></code></p></td>
+<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--profiling-layout</span> <span class="pre">PROFILING_LAYOUT</span> <span class="pre">[PROFILING_LAYOUT</span> <span class="pre">...]</span></code></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">&lt;prop1&gt;</span> <span class="pre">&lt;prop2&gt;</span></code> names of properties which need to be converted to a presence-absence profiling matrix of each value.</p></td>
 <td><p>presence/absence matrix; Array from ete4</p></td>
 <td><p>gradient of presence/total heatmap (only collapsed)</p></td>
 </tr>
-<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--categorical-matrix-layout</span> <span class="pre">CATEGORICAL_MATRIX_LAYOUT</span> <span class="pre">[CATEGORICAL_MATRIX_LAYOUT</span> <span class="pre">...]</span></code></p></td>
+<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--categorical-matrix-layout</span> <span class="pre">CATEGORICAL_MATRIX_LAYOUT</span> <span class="pre">[CATEGORICAL_MATRIX_LAYOUT</span> <span class="pre">...]</span></code></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">&lt;prop1&gt;</span> <span class="pre">&lt;prop2&gt;</span></code> names which need to be plotted as categorical_matrix_layout for categorical values.</p></td>
 <td><p>array from ete4</p></td>
 <td><p>None</p></td>
@@ -2131,7 +2214,7 @@ <h3><a class="toc-backref" href="#id45" role="doc-backlink">Layouts for categori
 </tbody>
 </table>
 <section id="lable-layout">
-<h4><a class="toc-backref" href="#id46" role="doc-backlink">Lable Layout</a><a class="headerlink" href="#lable-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id49" role="doc-backlink">Lable Layout</a><a class="headerlink" href="#lable-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--label-layout</span></code> will display the values of the given properties on the aligned panel. It will be shown as TextFace on leaf nodes and Stacked Horizontal RecFace on internal nodes.</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
@@ -2143,7 +2226,7 @@ <h4><a class="toc-backref" href="#id46" role="doc-backlink">Lable Layout</a><a c
 <img alt="label_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_label_layout.jpeg?raw=true" />
 </section>
 <section id="rectangle-layout">
-<h4><a class="toc-backref" href="#id47" role="doc-backlink">Rectangle Layout</a><a class="headerlink" href="#rectangle-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id50" role="doc-backlink">Rectangle Layout</a><a class="headerlink" href="#rectangle-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--rectangle-layout</span></code> will assign a color to each variable under the property, displaying as colored rectangle in aligned panel, when internal branches collapsed,  aligned panel shows the horizontal stacked bar to demostrate the composition of each variable.</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
@@ -2155,7 +2238,7 @@ <h4><a class="toc-backref" href="#id47" role="doc-backlink">Rectangle Layout</a>
 <img alt="rectangle_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_rectangular_layout.jpeg?raw=true" />
 </section>
 <section id="colorbranch-layout">
-<h4><a class="toc-backref" href="#id48" role="doc-backlink">ColorBranch Layout</a><a class="headerlink" href="#colorbranch-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id51" role="doc-backlink">ColorBranch Layout</a><a class="headerlink" href="#colorbranch-layout" title="Link to this heading">¶</a></h4>
 <p><cite>–colorbranch-layout</cite> will assign a color to each variable under the property, displaying as colored branch of corresponding node.</p>
 <p>Noted that in this case from leaf to root, if node contains the given property, it will still have the colored branch.</p>
 <p>Examples:</p>
@@ -2175,8 +2258,18 @@ <h4><a class="toc-backref" href="#id48" role="doc-backlink">ColorBranch Layout</
 </div>
 <img alt="colorbranch_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_colorbranch_layout_random.png?raw=true" />
 </section>
+<section id="bubble-layout">
+<h4><a class="toc-backref" href="#id52" role="doc-backlink">Bubble Layout</a><a class="headerlink" href="#bubble-layout" title="Link to this heading">¶</a></h4>
+<p><code class="docutils literal notranslate"><span class="pre">--bubble-layout</span></code> categorizes values of selected property by displaying color bubble on the corresponing leaf node.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
+<span class="o">-</span><span class="n">t</span> <span class="n">basic_example1_annotated</span><span class="o">.</span><span class="n">ete</span> \
+<span class="o">--</span><span class="n">bubble</span><span class="o">-</span><span class="n">layout</span> <span class="n">random_type</span>
+</pre></div>
+</div>
+<img alt="bubble_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_bubble_layout_randomtype.png?raw=true" />
+</section>
 <section id="background-layout">
-<h4><a class="toc-backref" href="#id49" role="doc-backlink">Background Layout</a><a class="headerlink" href="#background-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id53" role="doc-backlink">Background Layout</a><a class="headerlink" href="#background-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--background-layout</span></code> works just like <code class="docutils literal notranslate"><span class="pre">--colorbranch-layout</span></code>, the only difference is <code class="docutils literal notranslate"><span class="pre">--background-layout</span></code> visualize the background of the corresponding node instead of the branch color. It is useful and more visual when the tree is large.</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
@@ -2188,7 +2281,7 @@ <h4><a class="toc-backref" href="#id49" role="doc-backlink">Background Layout</a
 <img alt="background_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_background_layout.png?raw=true" />
 </section>
 <section id="piechart-layout">
-<h4><a class="toc-backref" href="#id50" role="doc-backlink">Piechart Layout</a><a class="headerlink" href="#piechart-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id54" role="doc-backlink">Piechart Layout</a><a class="headerlink" href="#piechart-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--piechart-layout</span></code> is unique layout designed for visualize internal nodes which contain counter of the given property from children nodes.</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
@@ -2200,7 +2293,7 @@ <h4><a class="toc-backref" href="#id50" role="doc-backlink">Piechart Layout</a><
 <img alt="piechart_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_piechart_layout.png?raw=true" />
 </section>
 <section id="profiling-layout">
-<h4><a class="toc-backref" href="#id51" role="doc-backlink">Profiling Layout</a><a class="headerlink" href="#profiling-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id55" role="doc-backlink">Profiling Layout</a><a class="headerlink" href="#profiling-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--profiling-layout</span></code> will convert categorical trait regardless <code class="docutils literal notranslate"><span class="pre">str</span></code> or <code class="docutils literal notranslate"><span class="pre">list</span></code> into presence-absence matrix. Importantly, once it collapsed, aligned matrix will show the gradient of presence/total of corresponding trait. This layout using draw_array algorithm from ete4 therefore it is s suitable for large scale.</p>
 <p>single value example</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># check metadata</span>
@@ -2240,12 +2333,12 @@ <h4><a class="toc-backref" href="#id51" role="doc-backlink">Profiling Layout</a>
 <img alt="profiling_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_profiling_layout_list.png?raw=true" />
 </section>
 <section id="categorical-matrix-layout">
-<h4><a class="toc-backref" href="#id52" role="doc-backlink">Categorical Matrix Layout</a><a class="headerlink" href="#categorical-matrix-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id56" role="doc-backlink">Categorical Matrix Layout</a><a class="headerlink" href="#categorical-matrix-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--categorical-matrix-layout</span></code> is similar to <code class="docutils literal notranslate"><span class="pre">--rectangle-layout</span></code> , which shows color block to represent the variable. But <code class="docutils literal notranslate"><span class="pre">--rectangle-layout</span></code> take <strong>EACH</strong> given column as one individual case as one layout, <code class="docutils literal notranslate"><span class="pre">--categorical-matrix-layout</span></code> take <strong>ALL</strong> given columns as one case to one layout.</p>
 </section>
 </section>
 <section id="layouts-for-boolean-data">
-<h3><a class="toc-backref" href="#id53" role="doc-backlink">Layouts for boolean data</a><a class="headerlink" href="#layouts-for-boolean-data" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id57" role="doc-backlink">Layouts for boolean data</a><a class="headerlink" href="#layouts-for-boolean-data" title="Link to this heading">¶</a></h3>
 <table class="docutils align-default">
 <thead>
 <tr class="row-odd"><th class="head"><p>Argument</p></th>
@@ -2283,7 +2376,7 @@ <h3><a class="toc-backref" href="#id53" role="doc-backlink">Layouts for boolean
 </tbody>
 </table>
 <section id="binary-layout">
-<h4><a class="toc-backref" href="#id54" role="doc-backlink">Binary Layout</a><a class="headerlink" href="#binary-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id58" role="doc-backlink">Binary Layout</a><a class="headerlink" href="#binary-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--binary-layout</span></code> highlights the positives. Each column has <strong>different</strong> colors. Internal node represent ratio of <strong>true/total gradient</strong>.</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
@@ -2295,7 +2388,7 @@ <h4><a class="toc-backref" href="#id54" role="doc-backlink">Binary Layout</a><a
 <img alt="binary_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_binary_layout.png?raw=true" />
 </section>
 <section id="binary-aggregate-layout">
-<h4><a class="toc-backref" href="#id55" role="doc-backlink">Binary Aggregate Layout</a><a class="headerlink" href="#binary-aggregate-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id59" role="doc-backlink">Binary Aggregate Layout</a><a class="headerlink" href="#binary-aggregate-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--binary-aggregate-layout</span></code> highlights the positives. Each column has <strong>different</strong> colors. Internal node present the <strong>accumulated counts of true</strong> and represent on color.</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
@@ -2307,7 +2400,7 @@ <h4><a class="toc-backref" href="#id55" role="doc-backlink">Binary Aggregate Lay
 <img alt="binary_layout2 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_binary_layout2.png?raw=true" />
 </section>
 <section id="binary-unicolor-layout">
-<h4><a class="toc-backref" href="#id56" role="doc-backlink">Binary Unicolor Layout</a><a class="headerlink" href="#binary-unicolor-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id60" role="doc-backlink">Binary Unicolor Layout</a><a class="headerlink" href="#binary-unicolor-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--binary-unicolor-layout</span></code> Each column has <strong>same</strong> colors. Internal node represent ratio of <strong>true/total gradient</strong>.</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
@@ -2319,7 +2412,7 @@ <h4><a class="toc-backref" href="#id56" role="doc-backlink">Binary Unicolor Layo
 <img alt="binary_layout3 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_binary_layout3.png?raw=true" />
 </section>
 <section id="binary-unicolor-aggregate-layout">
-<h4><a class="toc-backref" href="#id57" role="doc-backlink">Binary Unicolor Aggregate Layout</a><a class="headerlink" href="#binary-unicolor-aggregate-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id61" role="doc-backlink">Binary Unicolor Aggregate Layout</a><a class="headerlink" href="#binary-unicolor-aggregate-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--binary-unicolor-aggregate-layout</span></code> Each column has <strong>same</strong> colors. Internal node present the <strong>accumulated counts of true</strong> and represent on color.</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
@@ -2331,7 +2424,7 @@ <h4><a class="toc-backref" href="#id57" role="doc-backlink">Binary Unicolor Aggr
 <img alt="binary_layout4 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_binary_layout4.png?raw=true" />
 </section>
 <section id="binary-matrix-layout">
-<h4><a class="toc-backref" href="#id58" role="doc-backlink">Binary Matrix Layout</a><a class="headerlink" href="#binary-matrix-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id62" role="doc-backlink">Binary Matrix Layout</a><a class="headerlink" href="#binary-matrix-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--binary-matrix-layout</span></code> is similar to <code class="docutils literal notranslate"><span class="pre">--binary-layout</span></code> but using draw_array from ete4 therefore it ss suitable for large scale. But the limit is only work on rectangular tree</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
@@ -2344,7 +2437,7 @@ <h4><a class="toc-backref" href="#id58" role="doc-backlink">Binary Matrix Layout
 </section>
 </section>
 <section id="layouts-for-numerical-data">
-<h3><a class="toc-backref" href="#id59" role="doc-backlink">Layouts for Numerical data</a><a class="headerlink" href="#layouts-for-numerical-data" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id63" role="doc-backlink">Layouts for Numerical data</a><a class="headerlink" href="#layouts-for-numerical-data" title="Link to this heading">¶</a></h3>
 <p>Users can add the following arguments to use layouts for Numerical data</p>
 <table class="docutils align-default">
 <thead>
@@ -2403,7 +2496,7 @@ <h3><a class="toc-backref" href="#id59" role="doc-backlink">Layouts for Numerica
 </tbody>
 </table>
 <section id="id1">
-<h4><a class="toc-backref" href="#id60" role="doc-backlink">ColorBranch Layout</a><a class="headerlink" href="#id1" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id64" role="doc-backlink">ColorBranch Layout</a><a class="headerlink" href="#id1" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--colorbranch-layout</span></code> can detect if property is numerical data, then will color the branch based on color scale from minimum to maximum, including branches from the internal nodes. If internal nodes contain the corresponding property, then the relative value will be the representative; If not that the value will be the summarized value from descriptive statistic.</p>
 <p>Colorbranch with property that share from leaf to root:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># all nodes have dist value</span>
@@ -2427,8 +2520,8 @@ <h4><a class="toc-backref" href="#id60" role="doc-backlink">ColorBranch Layout</
 </div>
 <img alt="colorbranch_absdata example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_colorbranch_layout_support.png?raw=true" />
 </section>
-<section id="bubble-layout">
-<h4><a class="toc-backref" href="#id61" role="doc-backlink">Bubble Layout</a><a class="headerlink" href="#bubble-layout" title="Link to this heading">¶</a></h4>
+<section id="id2">
+<h4><a class="toc-backref" href="#id65" role="doc-backlink">Bubble Layout</a><a class="headerlink" href="#id2" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--bubble-layout</span></code> will scale the given absolute value property as size of bubble. Noted that if value is negative, bubble will be blue, otherwise bubble is red.</p>
 <p>If internal nodes contain the corresponding property, then the relative value will be the representative; If not that the value will be the summarized value from descriptive statistic.</p>
 <p>Bubble with property that share from leaf to root:</p>
@@ -2442,7 +2535,7 @@ <h4><a class="toc-backref" href="#id61" role="doc-backlink">Bubble Layout</a><a
 <img alt="bubble_sample example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_bubble_layout_sample1.png?raw=true" />
 </section>
 <section id="heatmap-layout">
-<h4><a class="toc-backref" href="#id62" role="doc-backlink">Heatmap Layout</a><a class="headerlink" href="#heatmap-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id66" role="doc-backlink">Heatmap Layout</a><a class="headerlink" href="#heatmap-layout" title="Link to this heading">¶</a></h4>
 <p>A series of heatmap layout is only the matter how to normalize the value to show the gradient of color.</p>
 <p><code class="docutils literal notranslate"><span class="pre">--heatmap-layout</span></code>  values will be normalized between 0 and 1 (minimu, maximum).</p>
 <p><code class="docutils literal notranslate"><span class="pre">--heatmap-mean-layout</span></code> values will be normalized between -1 and 1 by using the formula (val-mean)/(max-min)</p>
@@ -2470,10 +2563,11 @@ <h4><a class="toc-backref" href="#id62" role="doc-backlink">Heatmap Layout</a><a
 <img alt="heatmap_layout3 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_heatmap_layout3.png?raw=true" />
 </section>
 <section id="barplot-layout">
-<h4><a class="toc-backref" href="#id63" role="doc-backlink">Barplot Layout</a><a class="headerlink" href="#barplot-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id67" role="doc-backlink">Barplot Layout</a><a class="headerlink" href="#barplot-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--barplot-layout</span></code> will show the value as barplot, the length of barplot is the value of the property. will show barplot of numerical color. Noted that negative value won’t show in barplot</p>
 <p><code class="docutils literal notranslate"><span class="pre">--barplot-width</span></code> is the parameter to set the length of barplot, default is 200px.</p>
 <p><code class="docutils literal notranslate"><span class="pre">--barplot-scale</span></code> is the parameter to set the scale of barplot, if not given, the scale will be the maximum value of the property.</p>
+<p><code class="docutils literal notranslate"><span class="pre">--barplot-colorby</span></code> set the color of barplot by the a categorical property from metadata.[default: None]</p>
 <p>Examples:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
 <span class="o">-</span><span class="n">t</span> <span class="n">basic_example1_annotated</span><span class="o">.</span><span class="n">ete</span> \
@@ -2499,9 +2593,18 @@ <h4><a class="toc-backref" href="#id63" role="doc-backlink">Barplot Layout</a><a
 </div>
 <img alt="barplot_layout2 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_barplot_layout2.png?raw=true" />
 <img alt="barplot_layout3 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_barplot_layout3.png?raw=true" />
+<p>Noticed barplot in general is filled with one color for each column, using <cite>–barplot-colorby</cite> allows users to fill barplot based on other categorical data.</p>
+<p>here we color barplot <code class="docutils literal notranslate"><span class="pre">abs_data</span></code> by the categorical data <code class="docutils literal notranslate"><span class="pre">random_type</span></code></p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
+<span class="o">-</span><span class="n">t</span> <span class="n">basic_example1_annotated</span><span class="o">.</span><span class="n">ete</span> \
+<span class="o">--</span><span class="n">barplot</span><span class="o">-</span><span class="n">layout</span> <span class="n">abs_data</span> \
+<span class="o">--</span><span class="n">barplot</span><span class="o">-</span><span class="n">colorby</span> <span class="n">random_type</span>
+</pre></div>
+</div>
+<img alt="barplot_layout4 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_barplot_layout4.png?raw=true" />
 </section>
 <section id="numerical-matrix-layout">
-<h4><a class="toc-backref" href="#id64" role="doc-backlink">Numerical Matrix Layout</a><a class="headerlink" href="#numerical-matrix-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id68" role="doc-backlink">Numerical Matrix Layout</a><a class="headerlink" href="#numerical-matrix-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--numerical-matrix-layout</span></code> is similar to <code class="docutils literal notranslate"><span class="pre">--heatmap-layout</span></code> but using draw_array from ete4 therefore it is suitable for large scale, and also visualize data matrix which was stored as a file in previous annotation step.. But the limit is only work on rectangular tree.</p>
 <p>Here we example from <code class="docutils literal notranslate"><span class="pre">examples/basic_example0</span></code>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">head</span> <span class="n">data</span><span class="o">.</span><span class="n">array</span>
@@ -2542,7 +2645,7 @@ <h4><a class="toc-backref" href="#id64" role="doc-backlink">Numerical Matrix Lay
 </section>
 </section>
 <section id="layouts-for-analytical-data">
-<h3><a class="toc-backref" href="#id65" role="doc-backlink">Layouts for Analytical Data</a><a class="headerlink" href="#layouts-for-analytical-data" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id69" role="doc-backlink">Layouts for Analytical Data</a><a class="headerlink" href="#layouts-for-analytical-data" title="Link to this heading">¶</a></h3>
 <p>Users can add the following arguments to use layouts for Analytical data</p>
 <table class="docutils align-default">
 <thead>
@@ -2552,10 +2655,13 @@ <h3><a class="toc-backref" href="#id65" role="doc-backlink">Layouts for Analytic
 </thead>
 <tbody>
 <tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--acr-discrete-layout</span> <span class="pre">ACR_DISCRETE_LAYOUT</span> <span class="pre">[ACR_DISCRETE_LAYOUT</span> <span class="pre">...]</span></code></p></td>
-<td><p>&lt;prop1&gt; &lt;prop2&gt; names of properties which need to be plotted as acr-discrete-layout.</p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">&lt;prop1&gt;</span> <span class="pre">&lt;prop2&gt;</span></code> names of properties that need to be plotted as acr-discrete-layout.</p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--ls-layout</span> <span class="pre">LS_LAYOUT</span> <span class="pre">[LS_LAYOUT</span> <span class="pre">...]</span></code></p></td>
-<td><p>&lt;prop1&gt; &lt;prop2&gt; names of properties which need to be plotted as ls-layout.</p></td>
+<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--acr-continuous-layout</span> <span class="pre">ACR_CONTINUOUS_LAYOUT</span> <span class="pre">[ACR_CONTINUOUS_LAYOUT</span> <span class="pre">...]</span></code></p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">&lt;prop1&gt;</span> <span class="pre">&lt;prop2&gt;</span></code> names of properties that need to be plotted as acr-continuous-layout.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--ls-layout</span> <span class="pre">LS_LAYOUT</span> <span class="pre">[LS_LAYOUT</span> <span class="pre">...]</span></code></p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">&lt;prop1&gt;</span> <span class="pre">&lt;prop2&gt;</span></code> names of properties that need to be plotted as ls-layout.</p></td>
 </tr>
 </tbody>
 </table>
@@ -2575,7 +2681,7 @@ <h3><a class="toc-backref" href="#id65" role="doc-backlink">Layouts for Analytic
 </pre></div>
 </div>
 <section id="ancestral-character-reconstruction-and-phylogenetic-signal-layout">
-<h4><a class="toc-backref" href="#id66" role="doc-backlink">Ancestral Character Reconstruction and Phylogenetic Signal Layout</a><a class="headerlink" href="#ancestral-character-reconstruction-and-phylogenetic-signal-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id70" role="doc-backlink">Ancestral Character Reconstruction and Phylogenetic Signal Layout</a><a class="headerlink" href="#ancestral-character-reconstruction-and-phylogenetic-signal-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--acr-discrete-layout</span></code> is the layout designed for visualizing annotated tree of acr from previous annotate step or manual annotation. Noted that if phylogenetic signal test <code class="docutils literal notranslate"><span class="pre">--delta-stats</span></code> was executed, delta stat metric and p_value will be showed next to the root node.</p>
 <p>The infered character of each internal node will be shown as colorbranch, including the uncertain character</p>
 <p>We use example from <cite>examples/analytic_example</cite>:</p>
@@ -2588,7 +2694,7 @@ <h4><a class="toc-backref" href="#id66" role="doc-backlink">Ancestral Character
 <img alt="acr_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_acr_layout.png?raw=true" />
 </section>
 <section id="lineage-specificity-layout">
-<h4><a class="toc-backref" href="#id67" role="doc-backlink">Lineage Specificity Layout</a><a class="headerlink" href="#lineage-specificity-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id71" role="doc-backlink">Lineage Specificity Layout</a><a class="headerlink" href="#lineage-specificity-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--ls-layout</span></code> is used to visualized the output tree which was executed with <code class="docutils literal notranslate"><span class="pre">--ls-columns</span></code> in previous annotate step. Noted that Lineage Specificity Calculation computes three metric, which is:</p>
 <ul class="simple">
 <li><p><code class="docutils literal notranslate"><span class="pre">_f1</span></code>: f1 score</p></li>
@@ -2605,9 +2711,30 @@ <h4><a class="toc-backref" href="#id67" role="doc-backlink">Lineage Specificity
 <img alt="ls_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_ls_layout1.png?raw=true" />
 <img alt="ls_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_ls_layout2.png?raw=true" />
 </section>
+<section id="ancestral-character-reconstruction-for-continuous-traits">
+<h4><a class="toc-backref" href="#id72" role="doc-backlink">Ancestral Character Reconstruction for continuous traits</a><a class="headerlink" href="#ancestral-character-reconstruction-for-continuous-traits" title="Link to this heading">¶</a></h4>
+<p>Computing ACR for continuous traits:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">annotate</span> \
+<span class="o">-</span><span class="n">t</span> <span class="n">Anolis</span><span class="o">.</span><span class="n">tre</span> \
+<span class="o">--</span><span class="n">metadata</span> <span class="n">svl</span><span class="o">.</span><span class="n">csv</span> \
+<span class="o">-</span><span class="n">s</span> <span class="p">,</span> \
+<span class="o">--</span><span class="n">acr</span><span class="o">-</span><span class="n">continuous</span><span class="o">-</span><span class="n">columns</span> <span class="n">svl</span> \
+<span class="o">--</span><span class="n">prediction</span><span class="o">-</span><span class="n">method</span> <span class="n">BAYESIAN</span> \
+<span class="o">--</span><span class="n">model</span> <span class="n">OU</span> \
+<span class="o">--</span><span class="n">num</span><span class="o">-</span><span class="n">stat</span> <span class="n">none</span> \
+<span class="o">-</span><span class="n">o</span> <span class="o">./</span>
+
+
+<span class="n">treeprofiler</span> <span class="n">plot</span> \
+<span class="o">-</span><span class="n">t</span> <span class="n">Anolis_annotated</span><span class="o">.</span><span class="n">ete</span> \
+<span class="o">--</span><span class="n">acr</span><span class="o">-</span><span class="n">continuous</span><span class="o">-</span><span class="n">layout</span> <span class="n">svl</span>
+</pre></div>
+</div>
+<img alt="acr_continuous_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_acr_continuous_layout.png?raw=true" />
+</section>
 </section>
 <section id="layouts-for-multiple-sequence-alignment">
-<h3><a class="toc-backref" href="#id68" role="doc-backlink">Layouts for Multiple Sequence Alignment</a><a class="headerlink" href="#layouts-for-multiple-sequence-alignment" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id73" role="doc-backlink">Layouts for Multiple Sequence Alignment</a><a class="headerlink" href="#layouts-for-multiple-sequence-alignment" title="Link to this heading">¶</a></h3>
 <p>In order to visualize multiple sequence alignment alongside with the tree, first we need to annotate alignment using <code class="docutils literal notranslate"><span class="pre">--alignment</span></code> in <code class="docutils literal notranslate"><span class="pre">annotate</span></code>. Then activate alignment layout by adding <code class="docutils literal notranslate"><span class="pre">--alignment-layout</span></code>. Consensus sequence (if calculated) will shown once internal nodes collapsed.</p>
 <table class="docutils align-default">
 <thead>
@@ -2632,7 +2759,7 @@ <h3><a class="toc-backref" href="#id68" role="doc-backlink">Layouts for Multiple
 <img alt="msa_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_msa_layout.png?raw=true" />
 </section>
 <section id="layouts-for-eggnog-mapper-pfam-smart-annotations">
-<h3><a class="toc-backref" href="#id69" role="doc-backlink">Layouts for eggnog-mapper pfam/smart annotations</a><a class="headerlink" href="#layouts-for-eggnog-mapper-pfam-smart-annotations" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id74" role="doc-backlink">Layouts for eggnog-mapper pfam/smart annotations</a><a class="headerlink" href="#layouts-for-eggnog-mapper-pfam-smart-annotations" title="Link to this heading">¶</a></h3>
 <p>In order to visualize eggnog-mapper pfam/smart annotations alongside with the tree, first we need to annotate alignment using <code class="docutils literal notranslate"><span class="pre">--eggnog-mapper</span></code> in <code class="docutils literal notranslate"><span class="pre">annotate</span></code>. Then activate alignment layout by adding <code class="docutils literal notranslate"><span class="pre">--emapper-layout</span></code>.</p>
 <p>We use example in <code class="docutils literal notranslate"><span class="pre">examples/pratical_example/emapper</span></code>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># Visualize the tree with eggnog-mapper pfam/smart annotations</span>
@@ -2644,7 +2771,7 @@ <h3><a class="toc-backref" href="#id69" role="doc-backlink">Layouts for eggnog-m
 <img alt="domain_layout example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_domain_layout.png?raw=true" />
 </section>
 <section id="layouts-for-eggnog-mapper-functional-annotations">
-<h3><a class="toc-backref" href="#id70" role="doc-backlink">Layouts for eggnog-mapper functional annotations</a><a class="headerlink" href="#layouts-for-eggnog-mapper-functional-annotations" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id75" role="doc-backlink">Layouts for eggnog-mapper functional annotations</a><a class="headerlink" href="#layouts-for-eggnog-mapper-functional-annotations" title="Link to this heading">¶</a></h3>
 <p>If metadata is output from eggnog-mapper, using <code class="docutils literal notranslate"><span class="pre">--emapper-annotations</span></code> automatically parse all information as metadata. Program will parse data of all the columns from emapper output. Once tree is annotated, using <code class="docutils literal notranslate"><span class="pre">--emapper-layout</span></code> to visualize tree with all the metadata.</p>
 <table class="docutils align-default">
 <thead>
@@ -2673,7 +2800,7 @@ <h3><a class="toc-backref" href="#id70" role="doc-backlink">Layouts for eggnog-m
 <img alt="emapper_layout3 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_emapper_layout3.png?raw=true" />
 </section>
 <section id="layouts-for-taxonomy-annotation">
-<h3><a class="toc-backref" href="#id71" role="doc-backlink">Layouts for Taxonomy annotation</a><a class="headerlink" href="#layouts-for-taxonomy-annotation" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id76" role="doc-backlink">Layouts for Taxonomy annotation</a><a class="headerlink" href="#layouts-for-taxonomy-annotation" title="Link to this heading">¶</a></h3>
 <p>If target tree was annotated with <code class="docutils literal notranslate"><span class="pre">--taxon-column</span></code> in previous annotate step successfully, now activate Taxonomic layout using the following arguments to visualize taxonomic classification. All rank levels will be generated separately and users can switch each of them on/off.</p>
 <table class="docutils align-default">
 <thead>
@@ -2695,7 +2822,7 @@ <h3><a class="toc-backref" href="#id71" role="doc-backlink">Layouts for Taxonomy
 </table>
 <p>Only tree which was conducted with taxonomic annotation from treeprofiler in previous annotate step can use the taxonomic visualization.</p>
 <section id="taxonclade-layout">
-<h4><a class="toc-backref" href="#id72" role="doc-backlink">TaxonClade Layout</a><a class="headerlink" href="#taxonclade-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id77" role="doc-backlink">TaxonClade Layout</a><a class="headerlink" href="#taxonclade-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--taxonclade-layout</span></code> will assign different color to each taxa from each rank. Each rank will be a individual layout.</p>
 <p>we use example in <code class="docutils literal notranslate"><span class="pre">examples/taxonomy_example</span></code>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># Visualize the pre-annotated example archaea tree with taxonomic classification</span>
@@ -2707,7 +2834,7 @@ <h4><a class="toc-backref" href="#id72" role="doc-backlink">TaxonClade Layout</a
 <img alt="taxa_layout1 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_taxa_layout1.png?raw=true" />
 </section>
 <section id="taxonrectangle-layout">
-<h4><a class="toc-backref" href="#id73" role="doc-backlink">TaxonRectangle Layout</a><a class="headerlink" href="#taxonrectangle-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id78" role="doc-backlink">TaxonRectangle Layout</a><a class="headerlink" href="#taxonrectangle-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--taxonrectangle-layout</span></code> shows taxonomic classification as rectangular block from root to leaf.</p>
 <p>we use example in <code class="docutils literal notranslate"><span class="pre">examples/taxonomy_example</span></code>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># Visualize the pre-annotated example archaea tree with taxonomic classification</span>
@@ -2719,7 +2846,7 @@ <h4><a class="toc-backref" href="#id73" role="doc-backlink">TaxonRectangle Layou
 <img alt="taxa_layout2 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_taxa_layout2.png?raw=true" />
 </section>
 <section id="taxoncollapse-layout">
-<h4><a class="toc-backref" href="#id74" role="doc-backlink">TaxonCollapse Layout</a><a class="headerlink" href="#taxoncollapse-layout" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id79" role="doc-backlink">TaxonCollapse Layout</a><a class="headerlink" href="#taxoncollapse-layout" title="Link to this heading">¶</a></h4>
 <p><code class="docutils literal notranslate"><span class="pre">--taxoncollapse-layout</span></code> is similar to <code class="docutils literal notranslate"><span class="pre">--taxonrectangle-layout</span></code>, but it only show commen ancestor on one column in aligned panel which is shown as corresponding taxa from the rank. Users can switch which layout of rank to be visualized in control panel, once layout of rank is activated, tree will be collapsed based on the according rank. It is more accurate than <code class="docutils literal notranslate"><span class="pre">--taxonrectangle-layout</span></code> because it also shown the representative taxa in corresponding rank.</p>
 <p>we use example in <code class="docutils literal notranslate"><span class="pre">examples/taxonomy_example</span></code>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># Visualize the pre-annotated example archaea tree with taxonomic classification</span>
@@ -2735,7 +2862,7 @@ <h4><a class="toc-backref" href="#id74" role="doc-backlink">TaxonCollapse Layout
 </section>
 </section>
 <section id="customize-color-in-layout-with-color-config">
-<h3><a class="toc-backref" href="#id75" role="doc-backlink">Customize color in layout with color config</a><a class="headerlink" href="#customize-color-in-layout-with-color-config" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id80" role="doc-backlink">Customize color in layout with color config</a><a class="headerlink" href="#customize-color-in-layout-with-color-config" title="Link to this heading">¶</a></h3>
 <p>treeprofiler provides the option to cusomize the color on layouts:</p>
 <table class="docutils align-default">
 <thead>
@@ -2789,7 +2916,7 @@ <h3><a class="toc-backref" href="#id75" role="doc-backlink">Customize color in l
 </tbody>
 </table>
 <section id="basic-setting">
-<h4><a class="toc-backref" href="#id76" role="doc-backlink">Basic setting</a><a class="headerlink" href="#basic-setting" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id81" role="doc-backlink">Basic setting</a><a class="headerlink" href="#basic-setting" title="Link to this heading">¶</a></h4>
 <p>Here we will use the example from <code class="docutils literal notranslate"><span class="pre">examples/custom_color</span></code> , where the tree <code class="docutils literal notranslate"><span class="pre">basic_example1.nw</span></code> is annotated with <code class="docutils literal notranslate"><span class="pre">basic_example1_metadata1.tsv</span></code> and <code class="docutils literal notranslate"><span class="pre">basic_example1_metadata2.tsv</span></code>. Therefore the output tree is <code class="docutils literal notranslate"><span class="pre">basic_example1_annotated.ete</span></code> and <code class="docutils literal notranslate"><span class="pre">basic_example1_annotated.nw</span></code>.</p>
 <p>Check metadata</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">head</span> <span class="o">-</span><span class="mi">5</span> <span class="n">basic_example1_metadata1</span><span class="o">.</span><span class="n">tsv</span> <span class="n">basic_example1_metadata2</span><span class="o">.</span><span class="n">tsv</span>
@@ -2810,7 +2937,7 @@ <h4><a class="toc-backref" href="#id76" role="doc-backlink">Basic setting</a><a
 </pre></div>
 </div>
 <section id="customize-color-for-categorical-data">
-<h5><a class="toc-backref" href="#id77" role="doc-backlink">Customize color for categorical data</a><a class="headerlink" href="#customize-color-for-categorical-data" title="Link to this heading">¶</a></h5>
+<h5><a class="toc-backref" href="#id82" role="doc-backlink">Customize color for categorical data</a><a class="headerlink" href="#customize-color-for-categorical-data" title="Link to this heading">¶</a></h5>
 <p>Column <code class="docutils literal notranslate"><span class="pre">random_type</span></code> from the metadata is annotated as categorical data property called <code class="docutils literal notranslate"><span class="pre">random_type</span></code> in result tree <code class="docutils literal notranslate"><span class="pre">basic_example1_annotated.nw</span></code>. By default, all variables in col6 are: <code class="docutils literal notranslate"><span class="pre">high</span></code>, <code class="docutils literal notranslate"><span class="pre">medium</span></code> and <code class="docutils literal notranslate"><span class="pre">low</span></code>, so let’s customize the in <code class="docutils literal notranslate"><span class="pre">color.categorical.config</span></code> file:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># TreeProfiler Color Configuration</span>
 <span class="c1"># This file defines custom colors for properties of annotated tree nodes.</span>
@@ -2874,7 +3001,7 @@ <h5><a class="toc-backref" href="#id77" role="doc-backlink">Customize color for
 <img alt="plot_color_config2 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_color_config2.png?raw=true" />
 </section>
 <section id="customize-color-for-boolean-data">
-<h5><a class="toc-backref" href="#id78" role="doc-backlink">Customize color for boolean data</a><a class="headerlink" href="#customize-color-for-boolean-data" title="Link to this heading">¶</a></h5>
+<h5><a class="toc-backref" href="#id83" role="doc-backlink">Customize color for boolean data</a><a class="headerlink" href="#customize-color-for-boolean-data" title="Link to this heading">¶</a></h5>
 <p>Column <code class="docutils literal notranslate"><span class="pre">bool_type</span></code> and <code class="docutils literal notranslate"><span class="pre">bool_type2</span></code> are boolean data, therefore users can only decide the color representing True value. We stored the following config in <code class="docutils literal notranslate"><span class="pre">color.boolean.config</span></code></p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># TreeProfiler Color Configuration</span>
 <span class="c1"># This file defines custom colors for properties of annotated tree nodes.</span>
@@ -2903,7 +3030,7 @@ <h5><a class="toc-backref" href="#id78" role="doc-backlink">Customize color for
 <p>Noted that for boolean data, the color_config file should only contain the color for True value.</p>
 </section>
 <section id="customize-color-for-numerical-data">
-<h5><a class="toc-backref" href="#id79" role="doc-backlink">Customize color for numerical data</a><a class="headerlink" href="#customize-color-for-numerical-data" title="Link to this heading">¶</a></h5>
+<h5><a class="toc-backref" href="#id84" role="doc-backlink">Customize color for numerical data</a><a class="headerlink" href="#customize-color-for-numerical-data" title="Link to this heading">¶</a></h5>
 <p>We applied the color config to layouts for numerical data in <cite>color.numerical.config</cite> .</p>
 <p>We can still customize certain color for specific value.</p>
 <p>For example, we want to make make the heatmap layout with yellow color when value is <code class="docutils literal notranslate"><span class="pre">0</span></code>:</p>
@@ -2945,10 +3072,10 @@ <h5><a class="toc-backref" href="#id79" role="doc-backlink">Customize color for
 </section>
 </section>
 <section id="advanced-setting">
-<h4><a class="toc-backref" href="#id80" role="doc-backlink">Advanced Setting</a><a class="headerlink" href="#advanced-setting" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id85" role="doc-backlink">Advanced Setting</a><a class="headerlink" href="#advanced-setting" title="Link to this heading">¶</a></h4>
 <p>In the Basic setting, we only set the color for specific value, but in the Advanced setting, we can set the color for the range of value.</p>
 <section id="setting-color-range-for-numerical-data">
-<h5><a class="toc-backref" href="#id81" role="doc-backlink">Setting color range for numerical data</a><a class="headerlink" href="#setting-color-range-for-numerical-data" title="Link to this heading">¶</a></h5>
+<h5><a class="toc-backref" href="#id86" role="doc-backlink">Setting color range for numerical data</a><a class="headerlink" href="#setting-color-range-for-numerical-data" title="Link to this heading">¶</a></h5>
 <p>We can set the color range using <code class="docutils literal notranslate"><span class="pre">COLOR_MIN</span></code>, <code class="docutils literal notranslate"><span class="pre">COLOR_MAX</span></code>, <code class="docutils literal notranslate"><span class="pre">COLOR_MID</span></code> or <code class="docutils literal notranslate"><span class="pre">COLOR_NAN</span></code> under the column <code class="docutils literal notranslate"><span class="pre">CONDITION</span></code>.</p>
 <p>Here we set the color for the range of value in <cite>color.numerical2.config</cite>, noted that now the <code class="docutils literal notranslate"><span class="pre">VALUE</span></code> column is empty therefore the maximum value will be assigned to <code class="docutils literal notranslate"><span class="pre">COLOR_MAX</span></code>, the minimum value will be assigned to <code class="docutils literal notranslate"><span class="pre">COLOR_MIN</span></code>, and the middle value will be assigned to <code class="docutils literal notranslate"><span class="pre">COLOR_MID</span></code>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># TreeProfiler Color Configuration</span>
@@ -2978,7 +3105,7 @@ <h5><a class="toc-backref" href="#id81" role="doc-backlink">Setting color range
 <img alt="plot_color_config6 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_color_config6.png?raw=true" />
 </section>
 <section id="combining-settings-of-value-and-color-range-for-numerical-data">
-<h5><a class="toc-backref" href="#id82" role="doc-backlink">Combining settings of value and color range for numerical data</a><a class="headerlink" href="#combining-settings-of-value-and-color-range-for-numerical-data" title="Link to this heading">¶</a></h5>
+<h5><a class="toc-backref" href="#id87" role="doc-backlink">Combining settings of value and color range for numerical data</a><a class="headerlink" href="#combining-settings-of-value-and-color-range-for-numerical-data" title="Link to this heading">¶</a></h5>
 <p>In the previous example, we set the color range for the values, the value range is the range of minimum and maximum value by default, but we can also cusomize the value together with the color conditions</p>
 <p>Here we set the color for the range of value in <cite>color.numerical3.config</cite>, noted that now the <code class="docutils literal notranslate"><span class="pre">VALUE</span></code> column is not empty as we set the range from -5 to 5, therefore the value will be assigned to the corresponding color:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># TreeProfiler Color Configuration</span>
@@ -3033,7 +3160,7 @@ <h5><a class="toc-backref" href="#id82" role="doc-backlink">Combining settings o
 <img alt="plot_color_config8 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_color_config8.png?raw=true" />
 </section>
 <section id="wildcard-settings-of-color-range-for-numerical-matrix">
-<h5><a class="toc-backref" href="#id83" role="doc-backlink">Wildcard settings of color range for numerical matrix</a><a class="headerlink" href="#wildcard-settings-of-color-range-for-numerical-matrix" title="Link to this heading">¶</a></h5>
+<h5><a class="toc-backref" href="#id88" role="doc-backlink">Wildcard settings of color range for numerical matrix</a><a class="headerlink" href="#wildcard-settings-of-color-range-for-numerical-matrix" title="Link to this heading">¶</a></h5>
 <p>In the session of Layouts for numerical data, we describe the difference between <code class="docutils literal notranslate"><span class="pre">--heatmap-layout</span></code> and <code class="docutils literal notranslate"><span class="pre">--numerical-matrix-layout</span></code>. In short, <code class="docutils literal notranslate"><span class="pre">--heatmap-layout</span></code> treat each property individually therefore the range each column of heatmap is different, but <code class="docutils literal notranslate"><span class="pre">--numerical-matrix-layout</span></code> treat the whole matrix as a single property, therefore the range of value is the same for all columns.</p>
 <p>Therefore, when we set the color config for the numerical matrix layout, we can use the wildcard <code class="docutils literal notranslate"><span class="pre">*</span></code> to represent all the columns in the matrix.</p>
 <p>Here we set the color for the range of value in <cite>color.datamatrix.config</cite>, noted that now the <code class="docutils literal notranslate"><span class="pre">PROP</span></code> column is <code class="docutils literal notranslate"><span class="pre">*</span></code> which means all the columns in the matrix, therefore the value will be assigned to the corresponding color:</p>
@@ -3079,14 +3206,14 @@ <h5><a class="toc-backref" href="#id83" role="doc-backlink">Wildcard settings of
 <img alt="plot_color_config10 example" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_color_config10.png?raw=true" />
 </section>
 <section id="customize-color-settings-with-complex-conditions">
-<h5><a class="toc-backref" href="#id84" role="doc-backlink">Customize color settings with complex conditions</a><a class="headerlink" href="#customize-color-settings-with-complex-conditions" title="Link to this heading">¶</a></h5>
+<h5><a class="toc-backref" href="#id89" role="doc-backlink">Customize color settings with complex conditions</a><a class="headerlink" href="#customize-color-settings-with-complex-conditions" title="Link to this heading">¶</a></h5>
 <p>TBD</p>
 </section>
 </section>
 </section>
 </section>
 <section id="conditional-query-in-annotated-tree-can-be-used-in-both-annotate-and-plot">
-<h2><a class="toc-backref" href="#id85" role="doc-backlink">Conditional query in annotated tree (can be used in both annotate and plot)</a><a class="headerlink" href="#conditional-query-in-annotated-tree-can-be-used-in-both-annotate-and-plot" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id90" role="doc-backlink">Conditional query in annotated tree (can be used in both annotate and plot)</a><a class="headerlink" href="#conditional-query-in-annotated-tree-can-be-used-in-both-annotate-and-plot" title="Link to this heading">¶</a></h2>
 <p>TreeProfiler allows users to perform conditional process based on different circumstances:</p>
 <table class="docutils align-default">
 <thead>
@@ -3119,10 +3246,10 @@ <h2><a class="toc-backref" href="#id85" role="doc-backlink">Conditional query in
 </tbody>
 </table>
 <section id="query-syntax">
-<h3><a class="toc-backref" href="#id86" role="doc-backlink">Query Syntax</a><a class="headerlink" href="#query-syntax" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id91" role="doc-backlink">Query Syntax</a><a class="headerlink" href="#query-syntax" title="Link to this heading">¶</a></h3>
 <p>In this session we will use examples in <code class="docutils literal notranslate"><span class="pre">examples/automatic_query</span></code></p>
 <section id="basic-query-syntax">
-<h4><a class="toc-backref" href="#id87" role="doc-backlink">Basic Query Syntax</a><a class="headerlink" href="#basic-query-syntax" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id92" role="doc-backlink">Basic Query Syntax</a><a class="headerlink" href="#basic-query-syntax" title="Link to this heading">¶</a></h4>
 <p>All the conditional query shared the same syntax, a standard query consists the following</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">--</span><span class="n">pruned</span><span class="o">-</span><span class="n">by</span><span class="o">|</span><span class="n">collapsed</span><span class="o">-</span><span class="n">by</span><span class="o">|</span><span class="n">highlighted</span><span class="o">-</span><span class="n">by</span> <span class="s2">&quot;&lt;left_value&gt; &lt;operator&gt; &lt;right_value&gt;&quot;</span>
 </pre></div>
@@ -3145,7 +3272,7 @@ <h4><a class="toc-backref" href="#id87" role="doc-backlink">Basic Query Syntax</
 </tbody>
 </table>
 <section id="conditional-pruning">
-<h5><a class="toc-backref" href="#id88" role="doc-backlink">Conditional pruning</a><a class="headerlink" href="#conditional-pruning" title="Link to this heading">¶</a></h5>
+<h5><a class="toc-backref" href="#id93" role="doc-backlink">Conditional pruning</a><a class="headerlink" href="#conditional-pruning" title="Link to this heading">¶</a></h5>
 <p>Conditional pruning, prune leaf node whose name contain “FALPE”:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1">## annotate tree</span>
 <span class="n">treeprofiler</span> <span class="n">annotate</span> \
@@ -3164,7 +3291,7 @@ <h5><a class="toc-backref" href="#id88" role="doc-backlink">Conditional pruning<
 <img alt="pruned" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/prune.png?raw=true" />
 </section>
 <section id="conditional-highlight">
-<h5><a class="toc-backref" href="#id89" role="doc-backlink">Conditional highlight</a><a class="headerlink" href="#conditional-highlight" title="Link to this heading">¶</a></h5>
+<h5><a class="toc-backref" href="#id94" role="doc-backlink">Conditional highlight</a><a class="headerlink" href="#conditional-highlight" title="Link to this heading">¶</a></h5>
 <p>select tree node whose name contains <cite>FALPE</cite> character:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1">## annotate tree</span>
 <span class="n">treeprofiler</span> <span class="n">annotate</span> \
@@ -3201,7 +3328,7 @@ <h5><a class="toc-backref" href="#id89" role="doc-backlink">Conditional highligh
 </section>
 </section>
 <section id="query-in-internal-nodes">
-<h4><a class="toc-backref" href="#id90" role="doc-backlink">Query in internal nodes</a><a class="headerlink" href="#query-in-internal-nodes" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id95" role="doc-backlink">Query in internal nodes</a><a class="headerlink" href="#query-in-internal-nodes" title="Link to this heading">¶</a></h4>
 <p>Query in internal nodes’ properties is also available, in this case, <code class="docutils literal notranslate"><span class="pre">left_value</span></code> of query will be the internal node property, remember to add the proper suffixes such as <code class="docutils literal notranslate"><span class="pre">_avg</span></code>, <code class="docutils literal notranslate"><span class="pre">_max</span></code>,etc, for the numerical data or <cite>_counter</cite> for categorical and boolean data.</p>
 <p>Syntax for internal node numerical data:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># select tree internal node where sample1_avg feature &lt; 0.50</span>
@@ -3225,7 +3352,7 @@ <h4><a class="toc-backref" href="#id90" role="doc-backlink">Query in internal no
 <img alt="collapsed_counter" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/collapsed_counter.png?raw=true" />
 </section>
 <section id="and-and-or-conditions">
-<h4><a class="toc-backref" href="#id91" role="doc-backlink">AND and OR conditions</a><a class="headerlink" href="#and-and-or-conditions" title="Link to this heading">¶</a></h4>
+<h4><a class="toc-backref" href="#id96" role="doc-backlink">AND and OR conditions</a><a class="headerlink" href="#and-and-or-conditions" title="Link to this heading">¶</a></h4>
 <p>The syntax for the AND condition and OR condition in TreeProfiler is:</p>
 <p>AND condition will be under one argument, syntax seperated by <code class="docutils literal notranslate"><span class="pre">,</span></code>, such as:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># select tree  node where sample1 feature &gt; 0.50 AND sample2 &lt; 0.2</span>
@@ -3249,9 +3376,79 @@ <h4><a class="toc-backref" href="#id91" role="doc-backlink">AND and OR condition
 </div>
 <img alt="highlighted_or" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/highlighted_or.png?raw=true" />
 </section>
+<section id="conditional-query-with-config-file">
+<h4><a class="toc-backref" href="#id97" role="doc-backlink">Conditional query with config file</a><a class="headerlink" href="#conditional-query-with-config-file" title="Link to this heading">¶</a></h4>
+<p>In conditinary query, it also accept to use config to customize the highlighted and collapsed visualization. Example config file in <cite>color.config.template</cite>. It has the same structure as color config but the CONDITION column here is for operators as we mentioned in previous session.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>cat color.config.template`
+# TreeProfiler Conditional query Configuration
+# This file defines custom colors for properties of annotated tree nodes.
+# Columns: PROP, VALUE, COLOR, CONDITION
+
+# PROP: Property of the annotated tree node
+# VALUE: Value of the property to be colored
+# COLOR: Color to apply
+# CONDITION: operator
+
+PROP,VALUE,COLOR,CONDITION
+</pre></div>
+</div>
+<section id="highlight-with-custom-config">
+<h5><a class="toc-backref" href="#id98" role="doc-backlink">Highlight with custom config</a><a class="headerlink" href="#highlight-with-custom-config" title="Link to this heading">¶</a></h5>
+<p>we use example of <code class="docutils literal notranslate"><span class="pre">basic_example1.nw</span></code> and <code class="docutils literal notranslate"><span class="pre">basic_example1_metadata1.tsv</span></code>, we hope to highlight nodes whose <cite>random_type</cite> is <cite>low</cite> AND <cite>sample1</cite> greater than <cite>0.50</cite>, and we want to highlight those nodes in red.</p>
+<p>First we customize the config <code class="docutils literal notranslate"><span class="pre">color.config.query</span></code>:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># TreeProfiler Conditional query Configuration</span>
+<span class="c1"># This file defines custom colors for properties of annotated tree nodes.</span>
+<span class="c1"># Columns: PROP, VALUE, COLOR, CONDITION</span>
+
+<span class="c1"># PROP: Property of the annotated tree node</span>
+<span class="c1"># VALUE: Value of the property to be colored</span>
+<span class="c1"># COLOR: Color to apply</span>
+<span class="c1"># CONDITION: operator</span>
+
+<span class="n">PROP</span><span class="p">,</span><span class="n">VALUE</span><span class="p">,</span><span class="n">COLOR</span><span class="p">,</span><span class="n">CONDITION</span>
+<span class="n">random_type</span><span class="p">,</span><span class="n">low</span><span class="p">,</span><span class="n">red</span><span class="p">,</span><span class="o">=</span>
+<span class="n">sample1</span><span class="p">,</span><span class="mf">0.50</span><span class="p">,</span><span class="n">red</span><span class="p">,</span><span class="o">&gt;</span>
+</pre></div>
+</div>
+<p>we attach the config using the same <code class="docutils literal notranslate"><span class="pre">--highlighted-by</span></code>, dont forget about the <code class="docutils literal notranslate"><span class="pre">-s</span></code> to indicate the seperator</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
+<span class="o">-</span><span class="n">t</span> <span class="n">basic_example1_annotated</span><span class="o">.</span><span class="n">ete</span> \
+<span class="o">--</span><span class="n">highlighted</span><span class="o">-</span><span class="n">by</span> <span class="n">color</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">query</span> \
+<span class="o">-</span><span class="n">s</span> <span class="p">,</span>
+</pre></div>
+</div>
+<img alt="highlighted_query" src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/plot_query_config1.png?raw=true" />
+</section>
+<section id="collapse-with-custom-config">
+<h5><a class="toc-backref" href="#id99" role="doc-backlink">Collapse with custom config</a><a class="headerlink" href="#collapse-with-custom-config" title="Link to this heading">¶</a></h5>
+<p>Similar to <code class="docutils literal notranslate"><span class="pre">--highlighted-by</span></code>, in this case we try to collapse the internal nodes whose average of leaf properties <cite>sample1</cite> greater than <cite>0.50</cite>, with color of green.</p>
+<p>The config is in <code class="docutils literal notranslate"><span class="pre">color.config.collapsed</span></code></p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># TreeProfiler Conditional query Configuration</span>
+<span class="c1"># This file defines custom colors for properties of annotated tree nodes.</span>
+<span class="c1"># Columns: PROP, VALUE, COLOR, CONDITION</span>
+
+<span class="c1"># PROP: Property of the annotated tree node</span>
+<span class="c1"># VALUE: Value of the property to be colored</span>
+<span class="c1"># COLOR: Color to apply</span>
+<span class="c1"># CONDITION: operator</span>
+
+<span class="n">PROP</span><span class="p">,</span><span class="n">VALUE</span><span class="p">,</span><span class="n">COLOR</span><span class="p">,</span><span class="n">CONDITION</span>
+<span class="c1">#random_type_counter:high,0.35,red,&gt;</span>
+<span class="n">sample1_avg</span><span class="p">,</span><span class="mf">0.50</span><span class="p">,</span><span class="n">green</span><span class="p">,</span><span class="o">&gt;</span>
+</pre></div>
+</div>
+<p>example run</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">treeprofiler</span> <span class="n">plot</span> \
+<span class="o">-</span><span class="n">t</span> <span class="n">basic_example1_annotated</span><span class="o">.</span><span class="n">ete</span> \
+<span class="o">--</span><span class="n">collapsed</span><span class="o">-</span><span class="n">by</span> <span class="n">color</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">collapsed</span> \
+<span class="o">-</span><span class="n">s</span> <span class="p">,</span>
+</pre></div>
+</div>
+</section>
+</section>
 </section>
 <section id="conditional-limit-based-on-taxonomic-level">
-<h3><a class="toc-backref" href="#id92" role="doc-backlink">Conditional limit based on taxonomic level</a><a class="headerlink" href="#conditional-limit-based-on-taxonomic-level" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id100" role="doc-backlink">Conditional limit based on taxonomic level</a><a class="headerlink" href="#conditional-limit-based-on-taxonomic-level" title="Link to this heading">¶</a></h3>
 <p>Prune taxonomic annotated tree based on following taxonomic rank level,
 <code class="docutils literal notranslate"><span class="pre">kingdom</span></code>, <code class="docutils literal notranslate"><span class="pre">phylum</span></code>, <code class="docutils literal notranslate"><span class="pre">class</span></code>, <code class="docutils literal notranslate"><span class="pre">order</span></code>, <code class="docutils literal notranslate"><span class="pre">family</span></code>, <code class="docutils literal notranslate"><span class="pre">genus</span></code>, <code class="docutils literal notranslate"><span class="pre">species</span></code>, <code class="docutils literal notranslate"><span class="pre">subspecies</span></code></p>
 <p>case in GTDB in <code class="docutils literal notranslate"><span class="pre">examples/taxonomy_example/</span></code>:</p>
@@ -3276,7 +3473,7 @@ <h3><a class="toc-backref" href="#id92" role="doc-backlink">Conditional limit ba
 <p>As you see, class branches of target gtdb tree are all pruned and only left the internal branches which rank as class.</p>
 </section>
 <section id="choose-the-metric-for-internal-nodes-in-numerical-layout">
-<h3><a class="toc-backref" href="#id93" role="doc-backlink">Choose the metric for internal nodes in numerical layout</a><a class="headerlink" href="#choose-the-metric-for-internal-nodes-in-numerical-layout" title="Link to this heading">¶</a></h3>
+<h3><a class="toc-backref" href="#id101" role="doc-backlink">Choose the metric for internal nodes in numerical layout</a><a class="headerlink" href="#choose-the-metric-for-internal-nodes-in-numerical-layout" title="Link to this heading">¶</a></h3>
 <p>Internal nodes of numerical data are process descriptive statistic analysis by default, hence when users collapse any branch, barplot_layout or heatmap_layout will demonstrate representative value, <code class="docutils literal notranslate"><span class="pre">avg</span></code> by default. Representative value can be changed by using <code class="docutils literal notranslate"><span class="pre">--internal-plot-measure</span></code>.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># select max instead of avg as internal node plotting representative</span>
 <span class="n">treeprofiler</span> <span class="n">plot</span> \
@@ -3295,7 +3492,7 @@ <h3><a class="toc-backref" href="#id93" role="doc-backlink">Choose the metric fo
 </section>
 </section>
 <section id="demo1-explore-gtdb-taxonomic-tree-with-metadata-and-habitat-information-of-progenome3">
-<h2><a class="toc-backref" href="#id94" role="doc-backlink">Demo1 Explore GTDB taxonomic tree with metadata and habitat information of progenome3</a><a class="headerlink" href="#demo1-explore-gtdb-taxonomic-tree-with-metadata-and-habitat-information-of-progenome3" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id102" role="doc-backlink">Demo1 Explore GTDB taxonomic tree with metadata and habitat information of progenome3</a><a class="headerlink" href="#demo1-explore-gtdb-taxonomic-tree-with-metadata-and-habitat-information-of-progenome3" title="Link to this heading">¶</a></h2>
 <p>To illustrate the easiness and flexibility of TreeProfiler, we use it to annotate and visualize the version 202 of the GTDB prokaryotic phylogeny, which represents a species tree with 60,000 representative bacterial and archaeal species in <a class="reference external" href="https://data.gtdb.ecogenomic.org/releases/release202/">here</a>. GTDB provides the tree in plain newick format and massive datatable with various associated to such species. Apart from the metadata provided by the GTDB, here we also include annotations of genomes and species clusters to habitats from proGenomes3 (<a class="reference external" href="https://progenomes.embl.de/">Fullam et al. 2023</a>).</p>
 <p>Example can be found in directory <code class="docutils literal notranslate"><span class="pre">./examples/pratical/gtdb_r202/</span></code>. We already prepared the gtdb v202 taxonomic tree <code class="docutils literal notranslate"><span class="pre">gtdbv202.nw</span></code> by merging Bacteria and Archaea trees, detailed steps are included in <code class="docutils literal notranslate"><span class="pre">merge_gtdbtree.py</span></code>. Based on the difference of computational capacity, complete steps and pipeline can be found in <code class="docutils literal notranslate"><span class="pre">gtdbv202full_demo.sh</span></code> and <code class="docutils literal notranslate"><span class="pre">gtdbv202lite_demo.sh</span></code>.</p>
 <p>1) A glance of habitat information of progenome3</p>
@@ -3380,7 +3577,7 @@ <h2><a class="toc-backref" href="#id94" role="doc-backlink">Demo1 Explore GTDB t
 <p>Annotated tree and layouts can be shown as circular tree layout.</p>
 </section>
 <section id="demo2-explore-large-nifh-gene-tree-with-functional-and-taxonomic-information">
-<h2><a class="toc-backref" href="#id95" role="doc-backlink">Demo2 Explore large NifH gene tree with functional and taxonomic information</a><a class="headerlink" href="#demo2-explore-large-nifh-gene-tree-with-functional-and-taxonomic-information" title="Link to this heading">¶</a></h2>
+<h2><a class="toc-backref" href="#id103" role="doc-backlink">Demo2 Explore large NifH gene tree with functional and taxonomic information</a><a class="headerlink" href="#demo2-explore-large-nifh-gene-tree-with-functional-and-taxonomic-information" title="Link to this heading">¶</a></h2>
 <p>Here we analyzed the nitrogenase iron protein NifH gene family across bacteria from EggNOG6 with EggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments. TreeProfiler provides options which allows users to directly map EggNOG-mapper outputs including functional annotations and pfam/smart domain predictions. Hence are then able to map these functional annotations to their respective phylogenetic gene trees and them with the evolutionary history, tracing from leaf to root level.</p>
 <p>Map emapper annotation, pfam annotation and taxonomic annotation to target tree.</p>
 <p>Here we use example in <code class="docutils literal notranslate"><span class="pre">examples/pratical_example/emapper/</span></code>.</p>
@@ -3421,7 +3618,7 @@ <h2><a class="toc-backref" href="#id95" role="doc-backlink">Demo2 Explore large
           
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <h1 class="logo"><a href="index.html">treeprofiler</a></h1>
 
@@ -3432,7 +3629,16 @@ <h1 class="logo"><a href="index.html">treeprofiler</a></h1>
 
 
 
-<h3>Navigation</h3>
+
+<search id="searchbox" style="display: none" role="search">
+    <div class="searchformwrapper">
+    <form class="search" action="search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" placeholder="Search"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
 <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">TreeProfiler Tutorial</a></li>
@@ -3499,16 +3705,6 @@ <h3>Related Topics</h3>
   </ul></li>
 </ul>
 </div>
-<search id="searchbox" style="display: none" role="search">
-  <h3 id="searchlabel">Quick search</h3>
-    <div class="searchformwrapper">
-    <form class="search" action="search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
-      <input type="submit" value="Go" />
-    </form>
-    </div>
-</search>
-<script>document.getElementById('searchbox').style.display = "block"</script>
 
 
 
@@ -3525,8 +3721,8 @@ <h3 id="searchlabel">Quick search</h3>
       &#169;2024, Ziqi Deng & Jaime Huerta-Cepas.
       
       |
-      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.3.7</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.1.3</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
       
       |
       <a href="_sources/documentations.rst.txt"
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 7118636..bee813a 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -5,15 +5,16 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Index &#8212; treeprofiler [1.2.2-beta] documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d1102ebc" />
-    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=12dfc556" />
-    <script src="_static/documentation_options.js?v=fbc843e6"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
-    <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+    <link rel="stylesheet" type="text/css" href="static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="static/basic.css?v=686e5160" />
+    <link rel="stylesheet" type="text/css" href="static/alabaster.css?v=27fed22d" />
+    <script src="static/documentation_options.js?v=fbc843e6"></script>
+    <script src="static/doctools.js?v=9bcbadda"></script>
+    <script src="static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
   
 
   
@@ -41,7 +42,7 @@ <h1 id="index">Index</h1>
           
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <h1 class="logo"><a href="index.html">treeprofiler</a></h1>
 
@@ -52,7 +53,16 @@ <h1 class="logo"><a href="index.html">treeprofiler</a></h1>
 
 
 
-<h3>Navigation</h3>
+
+<search id="searchbox" style="display: none" role="search">
+    <div class="searchformwrapper">
+    <form class="search" action="search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" placeholder="Search"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
 <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="documentations.html">TreeProfiler Tutorial</a></li>
@@ -69,16 +79,6 @@ <h3>Related Topics</h3>
   </ul></li>
 </ul>
 </div>
-<search id="searchbox" style="display: none" role="search">
-  <h3 id="searchlabel">Quick search</h3>
-    <div class="searchformwrapper">
-    <form class="search" action="search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
-      <input type="submit" value="Go" />
-    </form>
-    </div>
-</search>
-<script>document.getElementById('searchbox').style.display = "block"</script>
 
 
 
@@ -95,8 +95,8 @@ <h3 id="searchlabel">Quick search</h3>
       &#169;2024, Ziqi Deng & Jaime Huerta-Cepas.
       
       |
-      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.3.7</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.1.3</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
       
     </div>
 
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index bb03f03..affa041 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -6,16 +6,17 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>Welcome to treeprofiler’s documentation! &#8212; treeprofiler [1.2.2-beta] documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d1102ebc" />
-    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=12dfc556" />
-    <script src="_static/documentation_options.js?v=fbc843e6"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
-    <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+    <link rel="stylesheet" type="text/css" href="static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="static/basic.css?v=686e5160" />
+    <link rel="stylesheet" type="text/css" href="static/alabaster.css?v=27fed22d" />
+    <script src="static/documentation_options.js?v=fbc843e6"></script>
+    <script src="static/doctools.js?v=9bcbadda"></script>
+    <script src="static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="TreeProfiler Tutorial" href="documentations.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
   
 
   
@@ -107,7 +108,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Li
           
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <h1 class="logo"><a href="#">treeprofiler</a></h1>
 
@@ -118,7 +119,16 @@ <h1 class="logo"><a href="#">treeprofiler</a></h1>
 
 
 
-<h3>Navigation</h3>
+
+<search id="searchbox" style="display: none" role="search">
+    <div class="searchformwrapper">
+    <form class="search" action="search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" placeholder="Search"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
 <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="documentations.html">TreeProfiler Tutorial</a></li>
@@ -136,16 +146,6 @@ <h3>Related Topics</h3>
   </ul></li>
 </ul>
 </div>
-<search id="searchbox" style="display: none" role="search">
-  <h3 id="searchlabel">Quick search</h3>
-    <div class="searchformwrapper">
-    <form class="search" action="search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
-      <input type="submit" value="Go" />
-    </form>
-    </div>
-</search>
-<script>document.getElementById('searchbox').style.display = "block"</script>
 
 
 
@@ -162,8 +162,8 @@ <h3 id="searchlabel">Quick search</h3>
       &#169;2024, Ziqi Deng & Jaime Huerta-Cepas.
       
       |
-      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.3.7</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.1.3</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
       
       |
       <a href="_sources/index.rst.txt"
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index 82085a2..6989b34 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -5,21 +5,22 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Search &#8212; treeprofiler [1.2.2-beta] documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d1102ebc" />
-    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=12dfc556" />
+    <link rel="stylesheet" type="text/css" href="static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="static/basic.css?v=686e5160" />
+    <link rel="stylesheet" type="text/css" href="static/alabaster.css?v=27fed22d" />
     
-    <script src="_static/documentation_options.js?v=fbc843e6"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
-    <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-    <script src="_static/searchtools.js"></script>
-    <script src="_static/language_data.js"></script>
+    <script src="static/documentation_options.js?v=fbc843e6"></script>
+    <script src="static/doctools.js?v=9bcbadda"></script>
+    <script src="static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="static/searchtools.js"></script>
+    <script src="static/language_data.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="#" />
     <script src="searchindex.js" defer="defer"></script>
     <meta name="robots" content="noindex" />
     
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
   
 
   
@@ -68,7 +69,7 @@ <h1 id="search-documentation">Search</h1>
           
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <h1 class="logo"><a href="index.html">treeprofiler</a></h1>
 
@@ -112,8 +113,8 @@ <h3>Related Topics</h3>
       &#169;2024, Ziqi Deng & Jaime Huerta-Cepas.
       
       |
-      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.3.7</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.1.3</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
       
     </div>
 
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index 3b94311..2ee6cd9 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"AND and OR conditions": [[0, "and-and-or-conditions"]], "Advanced Setting": [[0, "advanced-setting"]], "Analytical methods in treeProfiler": [[0, "analytical-methods-in-treeprofiler"]], "Ancestral Character Reconstruction and Phylogenetic Signal Layout": [[0, "ancestral-character-reconstruction-and-phylogenetic-signal-layout"]], "Ancestral character reconstruction": [[0, "ancestral-character-reconstruction"]], "Annotate metadata into tree": [[0, "annotate-metadata-into-tree"]], "Annotate metadata to internal nodes": [[0, "annotate-metadata-to-internal-nodes"]], "Annotating EggNOG-Mapper output and Domain information": [[0, "annotating-eggnog-mapper-output-and-domain-information"]], "Annotating Multiple Sequence Alignments(MSA)": [[0, "annotating-multiple-sequence-alignments-msa"]], "Background Layout": [[0, "background-layout"]], "Barplot Layout": [[0, "barplot-layout"]], "Basic Query Syntax": [[0, "basic-query-syntax"]], "Basic Usage": [[0, "basic-usage"]], "Basic metadata in TSV/CSV format": [[0, "basic-metadata-in-tsv-csv-format"]], "Basic options of visualizing layouts": [[0, "basic-options-of-visualizing-layouts"]], "Basic setting": [[0, "basic-setting"]], "Binary Aggregate Layout": [[0, "binary-aggregate-layout"]], "Binary Layout": [[0, "binary-layout"]], "Binary Matrix Layout": [[0, "binary-matrix-layout"]], "Binary Unicolor Aggregate Layout": [[0, "binary-unicolor-aggregate-layout"]], "Binary Unicolor Layout": [[0, "binary-unicolor-layout"]], "Bubble Layout": [[0, "bubble-layout"]], "Categorical Matrix Layout": [[0, "categorical-matrix-layout"]], "Choose the metric for internal nodes in numerical layout": [[0, "choose-the-metric-for-internal-nodes-in-numerical-layout"]], "ColorBranch Layout": [[0, "colorbranch-layout"], [0, "id1"]], "Combining settings of value and color range for numerical data": [[0, "combining-settings-of-value-and-color-range-for-numerical-data"]], "Conditional highlight": [[0, "conditional-highlight"]], "Conditional limit based on taxonomic level": [[0, "conditional-limit-based-on-taxonomic-level"]], "Conditional pruning": [[0, "conditional-pruning"]], "Conditional query in annotated tree (can be used in both annotate and plot)": [[0, "conditional-query-in-annotated-tree-can-be-used-in-both-annotate-and-plot"]], "Contents": [[0, "contents"]], "Contents:": [[1, null]], "Customize color for boolean data": [[0, "customize-color-for-boolean-data"]], "Customize color for categorical data": [[0, "customize-color-for-categorical-data"]], "Customize color for numerical data": [[0, "customize-color-for-numerical-data"]], "Customize color in layout with color config": [[0, "customize-color-in-layout-with-color-config"]], "Customize color settings with complex conditions": [[0, "customize-color-settings-with-complex-conditions"]], "Customizing summary methods for different columns": [[0, "customizing-summary-methods-for-different-columns"]], "Demo1 Explore GTDB taxonomic tree with metadata and habitat information of progenome3": [[0, "demo1-explore-gtdb-taxonomic-tree-with-metadata-and-habitat-information-of-progenome3"]], "Demo2 Explore large NifH gene tree with functional and taxonomic information": [[0, "demo2-explore-large-nifh-gene-tree-with-functional-and-taxonomic-information"]], "Dependencies": [[0, "dependencies"]], "Functional annotation": [[0, "functional-annotation"]], "Handling duplicated leaf names in metadata": [[0, "handling-duplicated-leaf-names-in-metadata"]], "Heatmap Layout": [[0, "heatmap-layout"]], "Identifying taxon names in different metadata fields/columns": [[0, "identifying-taxon-names-in-different-metadata-fields-columns"]], "Ignoring unclassified taxonomic annotations": [[0, "ignoring-unclassified-taxonomic-annotations"]], "Indices and tables": [[1, "indices-and-tables"]], "Input files": [[0, "input-files"]], "Install ETE v4": [[0, "install-ete-v4"]], "Install TreeProfiler": [[0, "install-treeprofiler"]], "Installation": [[0, "installation"]], "Interactive visualization interface": [[0, "interactive-visualization-interface"]], "Introduction": [[0, "introduction"]], "Lable Layout": [[0, "lable-layout"]], "Layouts for Analytical Data": [[0, "layouts-for-analytical-data"]], "Layouts for Multiple Sequence Alignment": [[0, "layouts-for-multiple-sequence-alignment"]], "Layouts for Numerical data": [[0, "layouts-for-numerical-data"]], "Layouts for Taxonomy annotation": [[0, "layouts-for-taxonomy-annotation"]], "Layouts for boolean data": [[0, "layouts-for-boolean-data"]], "Layouts for categorical data": [[0, "layouts-for-categorical-data"]], "Layouts for eggnog-mapper functional annotations": [[0, "layouts-for-eggnog-mapper-functional-annotations"]], "Layouts for eggnog-mapper pfam/smart annotations": [[0, "layouts-for-eggnog-mapper-pfam-smart-annotations"]], "Lineage Specificity Layout": [[0, "lineage-specificity-layout"]], "Lineage specificity analysis": [[0, "lineage-specificity-analysis"]], "Manual installation": [[0, "manual-installation"]], "Metadata TSV/CSV as a numerical data matrix": [[0, "metadata-tsv-csv-as-a-numerical-data-matrix"]], "Metadata without column names": [[0, "metadata-without-column-names"]], "Missing value detection": [[0, "missing-value-detection"]], "Numerical Matrix Layout": [[0, "numerical-matrix-layout"]], "Output formats for annotated trees": [[0, "output-formats-for-annotated-trees"]], "Phylogenetic signal delta statistic": [[0, "phylogenetic-signal-delta-statistic"]], "Piechart Layout": [[0, "piechart-layout"]], "Profiling Layout": [[0, "profiling-layout"]], "Query Syntax": [[0, "query-syntax"]], "Query in internal nodes": [[0, "query-in-internal-nodes"]], "Quick Start with examples dataset": [[0, "quick-start-with-examples-dataset"]], "Quick install via pip": [[0, "quick-install-via-pip"]], "Reading input tree": [[0, "reading-input-tree"]], "Rectangle Layout": [[0, "rectangle-layout"]], "Setting color range for numerical data": [[0, "setting-color-range-for-numerical-data"]], "Specifying data types for metadata columns": [[0, "specifying-data-types-for-metadata-columns"]], "Table of Contents": [[0, "table-of-contents"]], "TaxonClade Layout": [[0, "taxonclade-layout"]], "TaxonCollapse Layout": [[0, "taxoncollapse-layout"]], "TaxonRectangle Layout": [[0, "taxonrectangle-layout"]], "Taxonomic annotation": [[0, "taxonomic-annotation"]], "Tree format": [[0, "tree-format"]], "Tree parser": [[0, "tree-parser"]], "TreeProfiler Tutorial": [[0, "treeprofiler-tutorial"]], "Unmapped tree leaf property detection": [[0, "unmapped-tree-leaf-property-detection"]], "Using TreeProfiler": [[0, "using-treeprofiler"]], "Using different taxonomic databases from GTDB/NCBI": [[0, "using-different-taxonomic-databases-from-gtdb-ncbi"]], "Welcome to treeprofiler\u2019s documentation!": [[1, "welcome-to-treeprofiler-s-documentation"]], "Wildcard settings of color range for numerical matrix": [[0, "wildcard-settings-of-color-range-for-numerical-matrix"]], "emapper annotation output and the summary method": [[0, "id2"]], "treeprofiler-annotate computing phylogenetic profiles and annotation": [[0, "treeprofiler-annotate-computing-phylogenetic-profiles-and-annotation"]], "treeprofiler-plot visualizing phylogenetic profiles and annotation": [[0, "treeprofiler-plot-visualizing-phylogenetic-profiles-and-annotation"]]}, "docnames": ["documentations", "index"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["documentations.rst", "index.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": 0, "0": 0, "000": 0, "0000003": 0, "0000902": 0, "0000904": 0, "00018867741670758483": 0, "0002164578877048098": 0, "0002801019197914036": 0, "0003006": 0, "0003094673156738281": 0, "00043984526187224396": 0, "00048506476303705997": 0, "00048818236055906636": 0, "0005949760547048478": 0, "001": 0, "001324183303131325": 0, "00151915289715353": 0, "0019142742715016286": 0, "001965821926394849": 0, "001968860626220703": 0, "0034043477773810613": 0, "0056147812629824085": 0, "008000": 0, "00czay4286": 0, "00seay5240": 0, "01": 0, "011256165797407233": 0, "013434856612985015": 0, "015213913144468159": 0, "0195194146220156e": 0, "023102310231023": 0, "0244": 0, "027189256680401872": 0, "028430041000376213": 0, "036044144428": 0, "04825388395749479": 0, "04976016557186095": 0, "05": 0, "05160331726074219": 0, "05933033400048369": 0, "06": 0, "07": 0, "0732456957024559e": 0, "08034": 0, "09": 0, "098": 0, "0ustar": 0, "1": 0, "10": 0, "100": 0, "10000": 0, "10020": 0, "10090": 0, "115": 0, "115599899": 0, "117": 0, "117570": 0, "117571": 0, "117741186968884e": 0, "118": 0, "12": 0, "120": 0, "122": 0, "123": 0, "12655333321138568": 0, "127": 0, "128": 0, "13": 0, "131": 0, "131567": 0, "1338369": 0, "138": 0, "14": 0, "1437010": 0, "152tax": 0, "152tax_annot": 0, "15g": 0, "16": 0, "160049964146": 0, "169266432": 0, "17363108674806": 0, "175": 0, "186": 0, "188666": 0, "19": 0, "190563": 0, "194": 0, "1969": 0, "1970": 0, "1981": 0, "1987": 0, "1997": 0, "2": 0, "20": 0, "200": 0, "2000": 0, "2003": 0, "200px": 0, "2014": 0, "202": 0, "2023": 0, "207": 0, "207598": 0, "214": 0, "2172": 0, "2173": 0, "2174": 0, "2175": 0, "22": 0, "220": 0, "220000": 0, "23": 0, "245": 0, "248282": 0, "26": 0, "261": 0, "27": 0, "272": 0, "2759": 0, "276": 0, "28": 0, "29": 0, "2978723404255319": 0, "3": 0, "31": 0, "3100000000000005": 0, "3121192529798287": 0, "313833": 0, "314146": 0, "314293": 0, "314295": 0, "315846": 0, "318": 0, "32": 0, "3244296265415": 0, "32523": 0, "32524": 0, "32525": 0, "326": 0, "3276816717486982": 0, "33": 0, "33154": 0, "33208": 0, "33213": 0, "335": 0, "33511": 0, "349": 0, "35": 0, "356": 0, "362": 0, "366": 0, "376913": 0, "38": 0, "39": 0, "4": 0, "40": 0, "40674": 0, "41": 0, "42": 0, "43": 0, "44": 0, "447": 0, "45": 0, "45303222603186877": 0, "458698485629717e": 0, "46": 0, "463526916666666": 0, "471596": 0, "47894": 0, "479": 0, "49": 0, "494": 0, "5": 0, "50": 0, "5000": 0, "509": 0, "50px": 0, "51": 0, "5156064132880938": 0, "52": 0, "52340888828994": 0, "524138873540599": 0, "52779174042388": 0, "5384554640742852": 0, "56": 0, "585": 0, "591": 0, "6": 0, "60": 0, "6072": 0, "63": 0, "64": 0, "6552": 0, "667": 0, "67": 0, "671": 0, "676": 0, "683": 0, "684109": 0, "69": 0, "692277320371426": 0, "6g": 0, "7": 0, "70": 0, "713": 0, "73": 0, "73449420928955": 0, "746": 0, "74908423423767": 0, "767844": 0, "76837158203125e": 0, "7711": 0, "7739": 0, "7740000000000002": 0, "7742": 0, "7776": 0, "7817176831389784": 0, "79": 0, "792161": 0, "7955": 0, "8": 0, "805286": 0, "825": 0, "8287": 0, "86": 0, "8620000000000001": 0, "87": 0, "870000000000001": 0, "871": 0, "89": 0, "89593": 0, "898": 0, "9": 0, "906460531980665": 0, "92825": 0, "9347": 0, "937": 0, "9384942099527859": 0, "9443": 0, "9462054466377042": 0, "947": 0, "9473989345272481": 0, "9497450729621073": 0, "94cyaf6237": 0, "95": 0, "9526": 0, "9598": 0, "96": 0, "9604": 0, "9605": 0, "9606": 0, "96060539505257": 0, "96cmaj6134": 0, "97": 0, "9752818930521312": 0, "97cdaf6238": 0, "97cdaf6240": 0, "9801547427961053": 0, "98cmaj6932": 0, "98cmaj6933": 0, "99": 0, "9937640783202009": 0, "9999517018762923": 0, "A": 0, "And": 0, "As": 0, "At": 0, "But": 0, "By": 0, "For": 0, "If": 0, "In": 0, "It": 0, "Or": 0, "Such": 0, "The": 0, "Then": 0, "To": 0, "With": 0, "_annot": 0, "_annotated_prop2typ": 0, "_avg": 0, "_counter": 0, "_demo": 0, "_f1": 0, "_max": 0, "_min": 0, "_prec": 0, "_sen": 0, "_std": 0, "_sum": 0, "abl": 0, "abov": 0, "abs_data": 0, "abs_data2": 0, "absenc": 0, "absolut": 0, "acceler": 0, "access": 0, "accord": 0, "account": 0, "accpept": 0, "acctran": 0, "accumul": 0, "accur": 0, "acr": 0, "acr_discrete_column": 0, "acr_discrete_layout": 0, "across": 0, "action": 0, "activ": 0, "ad": 0, "adapt": 0, "add": 0, "adjust": 0, "adopt": 0, "africa": 0, "after": 0, "against": 0, "aim": 0, "al": 0, "albania": 0, "albanian": 0, "algorithm": 0, "align": 1, "all": 0, "allow": 0, "aln": 0, "along": 0, "alongsid": 0, "alreadi": 0, "also": 0, "altern": 0, "although": 0, "ambigu": 0, "amniota": 0, "among": 0, "an": 0, "analyt": 1, "analytic_exampl": 0, "analyz": 0, "ancestor": 0, "ani": 0, "annot": 1, "annotate_taxa": 0, "anntot": 0, "anoth": 0, "apart": 0, "app": 0, "appear": 0, "appil": 0, "appli": 0, "approach": 0, "approxim": 0, "aquatic_habitat": 0, "ar": 0, "ar122_metadata_r202": 0, "ar122_metadata_r202_lit": 0, "archaea": 0, "archaea_annot": 0, "archaeal": 0, "archiv": 0, "argument": 0, "arrai": 0, "array_avg": 0, "array_max": 0, "array_min": 0, "array_std": 0, "array_sum": 0, "assign": 0, "associ": 0, "attach": 0, "auto": 0, "automat": 0, "automatic_queri": 0, "avail": 0, "averag": 0, "avg": 0, "awk": 0, "b": 0, "bac120_metadata_r202": 0, "bac120_metadata_r202_lit": 0, "background_layout": 0, "bacteri": 0, "bacteria": 0, "bar": 0, "barplot_layout": 0, "base": 1, "basic": 1, "basic_example0": 0, "basic_example1": 0, "basic_example1_annot": 0, "basic_example1_metadata1": 0, "basic_example1_metadata2": 0, "basic_example1_prop2typ": 0, "basic_example2": 0, "becaus": 0, "becom": 0, "befor": 0, "being": 0, "below": 0, "besid": 0, "between": 0, "bigg_react": 0, "bilateria": 0, "billion": 0, "bin": 0, "binary_aggregate_layout": 0, "binary_layout": 0, "binary_matrix_layout": 0, "binary_unicolor_aggregate_layout": 0, "binary_unicolor_layout": 0, "biolog": 0, "biopython": 0, "black": 0, "blob": 0, "block": 0, "blue": 0, "bool": 0, "bool_prop": 0, "bool_prop_idx": 0, "bool_properti": 0, "bool_property_count": 0, "bool_typ": 0, "bool_type2": 0, "boolean": 1, "boreoeutheria": 0, "both": 1, "bottl": 0, "bottom": 0, "branch": 0, "brier": 0, "brite": 0, "brotli": 0, "bubble_layout": 0, "build": 0, "burn": 0, "button": 0, "c": 0, "c__heimdallarchaeia": 0, "c__korarchaeia": 0, "calcul": 0, "call": 0, "can": 1, "cantor": 0, "capac": 0, "case": 0, "cat": 0, "catarrhini": 0, "categor": 1, "categorci": 0, "categorical1": 0, "categorical1_count": 0, "categorical_dupl": 0, "categorical_matrix_layout": 0, "caus": 0, "cazi": 0, "cd": 0, "cellular": 0, "certain": 0, "chang": 0, "character_": 0, "character_countri": 0, "check": 0, "children": 0, "choos": 1, "chordata": 0, "circular": 0, "circumst": 0, "clade": 0, "class": 0, "classif": 0, "clone": 0, "close": 0, "cluster": 0, "code": 0, "cog_categori": 0, "col": 0, "col1": 0, "col1_avg": 0, "col1_max": 0, "col1_min": 0, "col1_std": 0, "col1_sum": 0, "col2": 0, "col2_avg": 0, "col3": 0, "col4": 0, "col5": 0, "col6": 0, "collaps": 0, "collapse_demo": 0, "color": 1, "color_config": 0, "color_max": 0, "color_mid": 0, "color_min": 0, "color_nan": 0, "colorbranch_layout": 0, "column_summary_method": 0, "columnnam": 0, "com": 0, "comman": 0, "command": 0, "commen": 0, "common_nam": 0, "compar": 0, "comparison": 0, "compgenomicslab": 0, "complet": 0, "composit": 0, "compress": 0, "comput": 1, "conda": 0, "condit": 1, "conduct": 0, "config": 1, "config_sep": 0, "configur": 0, "consensu": 0, "consesu": 0, "consid": 0, "consist": 0, "conson": 0, "construct": 0, "consult": 0, "contain": 0, "context": 0, "control": 0, "convert": 0, "copi": 0, "corner": 0, "correct": 0, "correctli": 0, "correspond": 0, "could": 0, "count": 0, "counter": 0, "countri": 0, "country_count": 0, "country_delta": 0, "country_pv": 0, "cover": 0, "cpu": 0, "craniata": 0, "creat": 0, "criteria": 0, "criterion": 0, "cross": 0, "cryptofilum": 0, "ctg": 0, "ctrl": 0, "current": 0, "cusom": 0, "cusomt": 0, "custom": 1, "custom_color": 0, "customdb": 0, "cut": 0, "cutoff": 0, "cython": 0, "d": 0, "d__archaea": 0, "data": 1, "data_2col": 0, "data_dir": 0, "data_matrix": 0, "datamatrix": 0, "dataset": 1, "datat": 0, "datatyp": 0, "db": 0, "de": 0, "debug": 0, "decid": 0, "decorate_gff": 0, "default": 0, "defin": 0, "degre": 0, "delai": 0, "delimit": 0, "deltran": 0, "demo": 0, "demo1": 1, "demo1_annot": 0, "demo1_prop2typ": 0, "demo2": 1, "demo2_annot": 0, "demo2_l": 0, "demo3": 0, "demo3_annot": 0, "demo4": 0, "demonstr": 0, "demostr": 0, "dengdenggtdb_genome_repres": 0, "dengzq1234": 0, "denovo": 0, "depend": 1, "dependeci": 0, "deploy": 0, "describ": 0, "descript": 0, "design": 0, "despit": 0, "detail": 0, "detech": 0, "determin": 0, "deuterostomia": 0, "dev": 0, "develop": 0, "deviat": 0, "diamond": 0, "diauxic": 0, "differen": 0, "dipnotetrapodomorpha": 0, "directli": 0, "directori": 0, "discret": 0, "disk": 0, "displai": 0, "dist": 0, "distanc": 0, "dmnd_algo": 0, "dmnd_ignore_warn": 0, "do": 0, "doe": 0, "doesn": 0, "done": 0, "down": 0, "download": 0, "downpass": 0, "draw_arrai": 0, "due": 0, "dump": 0, "dynam": 0, "e": 0, "each": 0, "easi": 0, "easili": 0, "easteurop": 0, "ec": 0, "ecogenom": 0, "editor": 0, "effect": 0, "effici": 0, "eft": 0, "eggnog": 1, "eggnog5": 0, "eggnog6": 0, "eggnog_og": 0, "either": 0, "electron": 0, "emapper_annot": 0, "emapper_demo": 0, "emapper_job": 0, "emapper_layout": 0, "emapper_pfam": 0, "emapper_smart": 0, "emapper_web_job": 0, "embed": 0, "embl": 0, "empti": 0, "enabl": 0, "encount": 0, "end": 0, "ensdarp00000116736": 0, "ensdorp00000023664": 0, "ent": 0, "entir": 0, "entropi": 0, "env": 0, "environ": 0, "ephrin_rec_lik": 0, "equal": 0, "equilibrium": 0, "error": 0, "estim": 0, "et": 1, "etc": 0, "ete4": 0, "etetoolkit": 0, "euarchontoglir": 0, "eukaryota": 0, "eumetazoa": 0, "euteleostomi": 0, "eutheria": 0, "evalu": 0, "even": 0, "everi": 0, "evolbioinfo": 0, "evoltyp": 0, "evolut": 0, "evolutionari": 0, "exact": 0, "exampl": 1, "example1": 0, "example1_demo": 0, "example2_demo": 0, "excel": 0, "execut": 0, "expect": 0, "experiment": 0, "explor": 1, "express": 0, "extract": 0, "f": 0, "f1": 0, "f81": 0, "f__kariarchaeacea": 0, "f__korarchaeacea": 0, "fa": 0, "faa": 0, "facilit": 0, "fact": 0, "falp": 0, "fals": 0, "famili": 0, "farri": 0, "fast": 0, "fasta": 0, "featur": 0, "feb": 0, "felsenstein": 0, "few": 0, "figur": 0, "figure1_al": 0, "file": 1, "filenam": 0, "filetyp": 0, "find": 0, "fine": 0, "first": 0, "fit": 0, "fix": 0, "flag": 0, "flask": 0, "flexibl": 0, "float": 0, "flua_h3_aa": 0, "focus": 0, "follow": 0, "forc": 0, "forg": 0, "forkserv": 0, "format": 1, "former": 0, "formula": 0, "found": 0, "framework": 0, "frequenc": 0, "ftp": 0, "full": 0, "fullam": 0, "fullfil": 0, "function": 1, "g": 0, "g__korarchaeum": 0, "g__lc": 0, "gascuel": 0, "gb_gca_003344655": 0, "gb_gca_011358815": 0, "gb_gca_014116815": 0, "gc_percentag": 0, "gcc": 0, "gcc_linux": 0, "gene": 1, "gener": 0, "genom": 0, "genome_s": 0, "genu": 0, "gini": 0, "git": 0, "github": 0, "given": 0, "glanc": 0, "global": 0, "gnathostomata": 0, "go": 0, "go_evid": 0, "gov": 0, "gradient": 0, "grain": 0, "graphic": 0, "greec": 0, "green": 0, "grei": 0, "group": 0, "gtdb": 1, "gtdb202dump": 0, "gtdb_demo": 0, "gtdb_example1": 0, "gtdb_id": 0, "gtdb_latest_dump": 0, "gtdb_r202": 0, "gtdb_taxid": 0, "gtdb_taxonomi": 0, "gtdb_v202": 0, "gtdb_v202_annot": 0, "gtdblatest": 0, "gtdbv202": 0, "gtdbv202_annot": 0, "gtdbv202full_demo": 0, "gtdbv202lite_demo": 0, "guaranti": 0, "gui": 0, "gz": 0, "ha": 0, "habitat": 1, "handi": 0, "haplorrhini": 0, "have": 0, "head": 0, "header": 0, "heatmap_layout": 0, "heatmap_mean_layout": 0, "heatmap_zscore_layout": 0, "heidelberg": 0, "help": 0, "henc": 0, "here": 0, "hex": 0, "high": 0, "highest": 0, "highli": 0, "highlight_demo": 0, "histori": 0, "hit": 0, "hky": 0, "hmmfrom": 0, "hmmto": 0, "home": 0, "hominida": 0, "hominina": 0, "hominoidea": 0, "homo": 0, "horizont": 0, "host_associ": 0, "how": 0, "howev": 0, "http": 0, "huge": 0, "i": 0, "id": 0, "idx": 0, "illustr": 0, "implement": 0, "importantli": 0, "improv": 0, "impur": 0, "includ": 0, "incompat": 0, "inconsist": 0, "independ": 0, "index": [0, 1], "individu": 0, "induc": 0, "infer": 0, "inform": 1, "infraord": 0, "input": 1, "input_tre": 0, "inrectli": 0, "instal": 1, "instead": 0, "int": 0, "integ": 0, "integr": 0, "interact": 1, "interfac": 1, "intern": 1, "internal_c": 0, "internal_nod": 0, "internal_pars": 0, "introduct": 1, "iron": 0, "is_albania": 0, "is_greec": 0, "iter": 0, "its": 0, "itwil": 0, "ityp": 0, "j": 0, "jc": 0, "joint": 0, "jtt": 0, "juke": 0, "just": 0, "keep": 0, "kegg": 0, "kegg_ko": 0, "kegg_modul": 0, "kegg_pathwai": 0, "kegg_rclass": 0, "kegg_react": 0, "kegg_tc": 0, "kei": 0, "kept": 0, "kind": 0, "kingdom": 0, "ko": 0, "l": 0, "label": 0, "label_layout": 0, "lambda0": 0, "larg": 1, "latest": 0, "latestest": 0, "latter": 0, "launch": 0, "layout": 1, "lazi": 0, "lca": 0, "leaf_nam": 0, "leafnam": 0, "least": 0, "leav": 0, "left": 0, "left_valu": 0, "legend": 0, "length": 0, "less": 0, "let": 0, "letter": 0, "level": 1, "librari": 0, "lightweight": 0, "like": 0, "likelihood": 0, "limit": 1, "line": 0, "linear": 0, "link": 0, "linux": 0, "list": 0, "list_data": 0, "load": 0, "load_metadata_to_tre": 0, "local": 0, "localhost": 0, "locat": 0, "log_likelihood": 0, "log_likelihood_restricted_joint": 0, "log_likelihood_restricted_map": 0, "log_likelihood_restricted_mppa": 0, "loos": 0, "low": 0, "ls_column": 0, "ls_layout": 0, "lse": 0, "m": 0, "maddison": 0, "mage_n": 0, "mai": 0, "main": 0, "mainli": 0, "make": 0, "mammalia": 0, "manual": 1, "map": 0, "mapper": 1, "margin": 0, "marginal_prob": 0, "marker": 0, "massiv": 0, "matplotlib": 0, "matter": 0, "max": 0, "max_annot_lvl": 0, "maximum": 0, "mcc_flua_h3": 0, "mcc_flua_h3_genotyp": 0, "mean": 0, "measur": 0, "medium": 0, "meet": 0, "memori": 0, "merg": 0, "merge_gtdbtre": 0, "metadata": 1, "metadata_sep": 0, "metadata_tab": 0, "metadata_tab_l": 0, "metazoa": 0, "method": 1, "method_": 0, "method_mppa": 0, "metric": 1, "metrix": 0, "middl": 0, "might": 0, "min": 0, "miniconda3": 0, "minim": 0, "minimap": 0, "minimu": 0, "minimum": 0, "minut": 0, "missing_gtdb_v202": 0, "missing_gtdb_v202_annot": 0, "missing_ncbi": 0, "ml": 0, "mm_knn6rw6j": 0, "mode": 0, "model": 0, "model_": 0, "model_f81": 0, "modul": [0, 1], "moment": 0, "mon": 0, "more": 0, "most": 0, "mp": 0, "mp_start_method": 0, "mppa": 0, "multipl": 1, "multiple_text_prop": 0, "multiple_text_properti": 0, "multiple_text_property_count": 0, "must": 0, "mutat": 0, "mute": 0, "n": 0, "n7739": 0, "n9598": 0, "named_lineag": 0, "namespac": 0, "nan": 0, "natur": 0, "navig": 0, "ncbi_annot": 0, "ncbi_assembly_level": 0, "ncbi_demo": 0, "ncbi_exampl": 0, "ncbi_genome_categori": 0, "ncbi_id": 0, "need": 0, "neg": 0, "nei": 0, "new": 0, "newick": 0, "next": 0, "nifh": 1, "nifh_annot": 0, "nih": 0, "nitrogenas": 0, "nleaf_a": 0, "nlm": 0, "node": 1, "node_1": 0, "node_2": 0, "node_3": 0, "node_4": 0, "node_5": 0, "non": 0, "none": 0, "normal": 0, "note": 0, "notic": 0, "novel": 0, "now": 0, "nrs_gcf_001560035": 0, "null": 0, "num": 0, "num_prop": 0, "num_prop_idx": 0, "num_scenario": 0, "num_serv": 0, "num_states_per_node_avg": 0, "num_unresolved_nod": 0, "numba": 0, "number": 0, "numer": 1, "numerical2": 0, "numerical3": 0, "numerical_matrix_layout": 0, "numerical_properti": 0, "numerical_property_avg": 0, "numerical_property_max": 0, "numerical_property_sum": 0, "numpi": 0, "nw": 0, "nwk": 0, "o": 0, "o__korarchaeal": 0, "o__uba460": 0, "obtain": 0, "off": 0, "onc": 0, "one": 0, "onli": 0, "oper": 0, "opisthokonta": 0, "optim": 0, "optimis": 0, "option": 1, "order": 0, "org": 0, "organ": 0, "ortholog": 0, "orthologi": 0, "other": 0, "otherwis": 0, "ouput": 0, "our": 0, "out": 0, "outdir": 0, "output": 1, "output_dir": 0, "overrid": 0, "overview": 0, "own": 0, "p": 0, "p__asgardarchaeota": 0, "p__thermoproteota": 0, "p_val": 0, "p_valu": 0, "packag": 0, "pad": 0, "page": 1, "panel": 0, "parallel": 0, "param": 0, "paramet": 0, "pars": 0, "parse_csv": 0, "parser": 1, "parsimoni": 0, "part": 0, "partial": 0, "parvord": 0, "pass": 0, "pastml": 0, "pastml2ete4": 0, "pastml_vers": 0, "path": 0, "per": 0, "percentag": 0, "percis": 0, "perform": 0, "pfam": 1, "pfam_realign": 0, "phy003i7zj_chick": 0, "phy004o1e0_aptfo": 0, "phy004pa1b_anapl": 0, "phy004tlna_apavi": 0, "phy00508fr_nipni": 0, "phy0054bo3_melga": 0, "phylogenei": 0, "phylogenet": 1, "phylogeni": 0, "phylum": 0, "phylumn": 0, "pident": 0, "piechart_layout": 0, "piechartfac": 0, "pip": 1, "pipelin": 0, "plain": 0, "platform": 0, "pleas": 0, "plot": 1, "plu": 0, "png": 0, "posit": 0, "possibl": 0, "posterior": 0, "posteriori": 0, "pratic": 0, "pratical_exampl": 0, "pre": 0, "prec": 0, "prec_cutoff": 0, "precis": 0, "precomput": 0, "predefin": 0, "predict": 0, "preferred_nam": 0, "prepar": 0, "presenc": 0, "present": 0, "preset": 0, "press": 0, "previou": 0, "primat": 0, "print": 0, "priorit": 0, "prioritis": 0, "probabilist": 0, "probabl": 0, "process": 0, "produc": 0, "product": 0, "profil": 1, "profile1": 0, "profile1_count": 0, "profile1_f1": 0, "profile1_prec": 0, "profile1_sen": 0, "profiling_layout": 0, "progenome3": 1, "progenome_demo": 0, "progenomes3": 0, "program": 0, "prokaryot": 0, "prop": 0, "prop1": 0, "prop2": 0, "prop2typ": 0, "prop2type_fil": 0, "prop_nam": 0, "propab": 0, "propabl": 0, "proper": 0, "properli": 0, "propertii": 0, "property_nam": 0, "proport": 0, "protein": 0, "protein_count": 0, "provid": 0, "prthologi": 0, "prune_demo": 0, "ptn": 0, "pub": 0, "pupko": 0, "put": 0, "px": 0, "py": 0, "pyqt": 0, "python": 0, "q": 0, "queri": 1, "query_cov": 0, "query_coverag": 0, "query_length": 0, "query_nam": 0, "quick": 1, "quit": 0, "r": 0, "ram": 0, "random_column1": 0, "random_column1_avg": 0, "random_column1_max": 0, "random_column1_min": 0, "random_column1_std": 0, "random_column1_sum": 0, "random_column2": 0, "random_column2_avg": 0, "random_column3": 0, "random_column3_avg": 0, "random_column3_sum": 0, "random_typ": 0, "random_type_count": 0, "rank": 0, "rank_limit": 0, "rate": 0, "ratio": 0, "raw": 0, "read": 1, "real": 0, "reccomend": 0, "recfac": 0, "recommend": 0, "recov": 0, "rectangle_layout": 0, "rectangular": 0, "rectfac": 0, "red": 0, "reduc": 0, "ref": 0, "refer": 0, "reflect": 0, "regardless": 0, "reinstal": 0, "rel": 0, "relat": 0, "relationship": 0, "releas": 0, "release202": 0, "rememb": 0, "remov": 0, "render": 0, "replac": 0, "repo": 0, "report_ortholog": 0, "repositori": 0, "repres": 0, "represent": 0, "requir": 0, "rerun": 0, "resolv": 0, "resourc": 0, "respect": 0, "result": 0, "resum": 0, "return": 0, "revers": 0, "right": 0, "right_valu": 0, "root": 0, "row": 0, "rs_gcf_000019605": 0, "rs_gcf_000730245": 0, "rs_gcf_001560035": 0, "rs_gcf_003948265": 0, "rs_gcf_004210275": 0, "run": 0, "s__korarchaeum": 0, "s__lc": 0, "salmon": 0, "same": 0, "sample1": 0, "sample1_avg": 0, "sample2": 0, "sample3": 0, "sample4": 0, "sample5": 0, "sapien": 0, "sarat": 0, "sarcopterygii": 0, "scale": 0, "scan": 0, "scenario": 0, "sci_nam": 0, "scipi": 0, "score": 0, "script": 0, "se": 0, "search": [0, 1], "second": 0, "see": 0, "seed_ortholog": 0, "select": 0, "selenium": 0, "sen": 0, "sens_cutoff": 0, "sensit": 0, "sep": 0, "separ": 0, "seper": 0, "seqfrom": 0, "seqto": 0, "sequenc": 1, "seri": 0, "serv": 0, "server": 0, "session": 0, "setup": 0, "sh": 0, "shannon": 0, "share": 0, "shm": 0, "short": 0, "should": 0, "show": 0, "show_tree_prop": 0, "shown": 0, "signific": 0, "simiiform": 0, "similar": 0, "simpli": 0, "singl": 0, "situat": 0, "size": 0, "smaller": 0, "smart": 1, "smartview": 0, "so": 0, "softwar": 0, "soil_habitat": 0, "solut": 0, "solv": 0, "some": 0, "sometim": 0, "sourc": 0, "sp001940725": 0, "space": 0, "speci": 0, "special": 0, "ss": 0, "stack": 0, "standard": 0, "standpoint": 0, "start": 1, "stat": 0, "state": 0, "std": 0, "steel": 0, "step": 0, "still": 0, "store": 0, "str": 0, "strategi": 0, "string": 0, "structur": 0, "sub": 0, "subcommand": 0, "subfamili": 0, "subject_cov": 0, "subord": 0, "subphylum": 0, "subset": 0, "subspeci": 0, "subtre": 0, "successfulli": 0, "sucessfulli": 0, "suffix": 0, "suitabl": 0, "sum": 0, "sum_scor": 0, "summar": 0, "summur": 0, "superclass": 0, "superfamili": 0, "superkingdom": 0, "superord": 0, "support": 0, "switch": 0, "swofford": 0, "symbol": 0, "syntax": 1, "t": 0, "tab": 0, "table1": 0, "table2": 0, "tag": 0, "take": 0, "tar": 0, "target": 0, "target_ortholog": 0, "tax_scop": 0, "taxa": 0, "taxa_0": 0, "taxa_1": 0, "taxa_2": 0, "taxa_3": 0, "taxa_4": 0, "taxa_dump": 0, "taxa_field": 0, "taxadb": 0, "taxadump": 0, "taxdump": 0, "taxid": 0, "taxon_column": 0, "taxon_delimit": 0, "taxonom": 1, "taxonomi": 1, "taxonomy_exampl": 0, "tbd": 0, "teleostomi": 0, "tell": 0, "temp_dir": 0, "templat": 0, "term": 0, "termin": 0, "test": 0, "tetrapoda": 0, "text": 0, "text_prop": 0, "text_prop_idx": 0, "text_properti": 0, "text_property_count": 0, "textfac": 0, "than": 0, "thei": 0, "them": 0, "theoret": 0, "therefor": 0, "theria": 0, "thi": 0, "thin": 0, "thread": 0, "three": 0, "threshold": 0, "time": 0, "tip": 0, "titl": 0, "togeth": 0, "tool": 0, "toolkit": 0, "top": 0, "total": 0, "trace": 0, "trait": 0, "transfer": 0, "transform": 0, "trati": 0, "travers": 0, "treat": 0, "tree": 1, "tree_annot": 0, "treeprofielr": 0, "treeprofiler_galleri": 0, "true": 0, "tsv0000664000175000017500000343216414447266674012351": 0, "tutori": 1, "two": 0, "txt": 0, "typic": 0, "u": 0, "unannot": 0, "uncertain": 0, "under": 0, "uniqu": 0, "univers": 0, "unknown": 0, "up": 0, "updat": 0, "us": 1, "usag": 1, "user": 0, "user_data": 0, "v1": 0, "v202": 0, "v4": 1, "val": 0, "variabl": 0, "variou": 0, "veri": 0, "version": 0, "vertebrata": 0, "vertic": 0, "via": 1, "view": 0, "violat": 0, "visual": 1, "visualis": 0, "visul": 0, "vowel": 0, "w": 0, "wa": 0, "wai": 0, "want": 0, "warn": 0, "we": 0, "westeurop": 0, "wget": 0, "when": 0, "where": 0, "which": 0, "while": 0, "white": 0, "whole": 0, "whose": 0, "width": 0, "within": 0, "won": 0, "word": 0, "work": 0, "would": 0, "wsgi": 0, "wt": 0, "www": 0, "x": 0, "xf": 0, "xfam": 0, "xp_002609184": 0, "xth": 0, "y": 0, "ye": 0, "yellow": 0, "you": 0, "your": 0, "z": 0, "zcat": 0, "zero": 0, "zhang": 0, "zip": 0, "zoom": 0, "zscore": 0}, "titles": ["TreeProfiler Tutorial", "Welcome to treeprofiler\u2019s documentation!"], "titleterms": {"": 1, "AND": 0, "OR": 0, "advanc": 0, "aggreg": 0, "align": 0, "analysi": 0, "analyt": 0, "ancestr": 0, "annot": 0, "background": 0, "barplot": 0, "base": 0, "basic": 0, "binari": 0, "boolean": 0, "both": 0, "bubbl": 0, "can": 0, "categor": 0, "charact": 0, "choos": 0, "color": 0, "colorbranch": 0, "column": 0, "combin": 0, "complex": 0, "comput": 0, "condit": 0, "config": 0, "content": [0, 1], "csv": 0, "custom": 0, "data": 0, "databas": 0, "dataset": 0, "delta": 0, "demo1": 0, "demo2": 0, "depend": 0, "detect": 0, "differ": 0, "document": 1, "domain": 0, "duplic": 0, "eggnog": 0, "emapp": 0, "et": 0, "exampl": 0, "explor": 0, "field": 0, "file": 0, "format": 0, "from": 0, "function": 0, "gene": 0, "gtdb": 0, "habitat": 0, "handl": 0, "heatmap": 0, "highlight": 0, "identifi": 0, "ignor": 0, "indic": 1, "inform": 0, "input": 0, "instal": 0, "interact": 0, "interfac": 0, "intern": 0, "introduct": 0, "labl": 0, "larg": 0, "layout": 0, "leaf": 0, "level": 0, "limit": 0, "lineag": 0, "manual": 0, "mapper": 0, "matrix": 0, "metadata": 0, "method": 0, "metric": 0, "miss": 0, "msa": 0, "multipl": 0, "name": 0, "ncbi": 0, "nifh": 0, "node": 0, "numer": 0, "option": 0, "output": 0, "parser": 0, "pfam": 0, "phylogenet": 0, "piechart": 0, "pip": 0, "plot": 0, "profil": 0, "progenome3": 0, "properti": 0, "prune": 0, "queri": 0, "quick": 0, "rang": 0, "read": 0, "reconstruct": 0, "rectangl": 0, "sequenc": 0, "set": 0, "signal": 0, "smart": 0, "specif": 0, "specifi": 0, "start": 0, "statist": 0, "summari": 0, "syntax": 0, "tabl": [0, 1], "taxon": 0, "taxonclad": 0, "taxoncollaps": 0, "taxonom": 0, "taxonomi": 0, "taxonrectangl": 0, "tree": 0, "treeprofil": [0, 1], "tsv": 0, "tutori": 0, "type": 0, "unclassifi": 0, "unicolor": 0, "unmap": 0, "us": 0, "usag": 0, "v4": 0, "valu": 0, "via": 0, "visual": 0, "welcom": 1, "wildcard": 0, "without": 0}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"ACR for contiunous data": [[0, "acr-for-contiunous-data"]], "AND and OR conditions": [[0, "and-and-or-conditions"]], "Advanced Setting": [[0, "advanced-setting"]], "Analytical methods in treeProfiler": [[0, "analytical-methods-in-treeprofiler"]], "Ancestral Character Reconstruction and Phylogenetic Signal Layout": [[0, "ancestral-character-reconstruction-and-phylogenetic-signal-layout"]], "Ancestral Character Reconstruction for continuous traits": [[0, "ancestral-character-reconstruction-for-continuous-traits"]], "Ancestral character reconstruction": [[0, "ancestral-character-reconstruction"]], "Annotate metadata into tree": [[0, "annotate-metadata-into-tree"]], "Annotate metadata to internal nodes": [[0, "annotate-metadata-to-internal-nodes"]], "Annotating EggNOG-Mapper output and Domain information": [[0, "annotating-eggnog-mapper-output-and-domain-information"]], "Annotating Multiple Sequence Alignments(MSA)": [[0, "annotating-multiple-sequence-alignments-msa"]], "Background Layout": [[0, "background-layout"]], "Barplot Layout": [[0, "barplot-layout"]], "Basic Query Syntax": [[0, "basic-query-syntax"]], "Basic Usage": [[0, "basic-usage"]], "Basic metadata in TSV/CSV format": [[0, "basic-metadata-in-tsv-csv-format"]], "Basic options of visualizing layouts": [[0, "basic-options-of-visualizing-layouts"]], "Basic setting": [[0, "basic-setting"]], "Binary Aggregate Layout": [[0, "binary-aggregate-layout"]], "Binary Layout": [[0, "binary-layout"]], "Binary Matrix Layout": [[0, "binary-matrix-layout"]], "Binary Unicolor Aggregate Layout": [[0, "binary-unicolor-aggregate-layout"]], "Binary Unicolor Layout": [[0, "binary-unicolor-layout"]], "Bubble Layout": [[0, "bubble-layout"], [0, "id2"]], "Categorical Matrix Layout": [[0, "categorical-matrix-layout"]], "Choose the metric for internal nodes in numerical layout": [[0, "choose-the-metric-for-internal-nodes-in-numerical-layout"]], "Collapse with custom config": [[0, "collapse-with-custom-config"]], "ColorBranch Layout": [[0, "colorbranch-layout"], [0, "id1"]], "Combining settings of value and color range for numerical data": [[0, "combining-settings-of-value-and-color-range-for-numerical-data"]], "Conditional highlight": [[0, "conditional-highlight"]], "Conditional limit based on taxonomic level": [[0, "conditional-limit-based-on-taxonomic-level"]], "Conditional pruning": [[0, "conditional-pruning"]], "Conditional query in annotated tree (can be used in both annotate and plot)": [[0, "conditional-query-in-annotated-tree-can-be-used-in-both-annotate-and-plot"]], "Conditional query with config file": [[0, "conditional-query-with-config-file"]], "Contents": [[0, "contents"]], "Contents:": [[1, null]], "Customize color for boolean data": [[0, "customize-color-for-boolean-data"]], "Customize color for categorical data": [[0, "customize-color-for-categorical-data"]], "Customize color for numerical data": [[0, "customize-color-for-numerical-data"]], "Customize color in layout with color config": [[0, "customize-color-in-layout-with-color-config"]], "Customize color settings with complex conditions": [[0, "customize-color-settings-with-complex-conditions"]], "Customizing summary methods for different columns": [[0, "customizing-summary-methods-for-different-columns"]], "Demo1 Explore GTDB taxonomic tree with metadata and habitat information of progenome3": [[0, "demo1-explore-gtdb-taxonomic-tree-with-metadata-and-habitat-information-of-progenome3"]], "Demo2 Explore large NifH gene tree with functional and taxonomic information": [[0, "demo2-explore-large-nifh-gene-tree-with-functional-and-taxonomic-information"]], "Dependencies": [[0, "dependencies"]], "Functional annotation": [[0, "functional-annotation"]], "Handling duplicated leaf names in metadata": [[0, "handling-duplicated-leaf-names-in-metadata"]], "Heatmap Layout": [[0, "heatmap-layout"]], "Highlight with custom config": [[0, "highlight-with-custom-config"]], "Identifying taxon names in different metadata fields/columns": [[0, "identifying-taxon-names-in-different-metadata-fields-columns"]], "Ignoring unclassified taxonomic annotations": [[0, "ignoring-unclassified-taxonomic-annotations"]], "Indices and tables": [[1, "indices-and-tables"]], "Input files": [[0, "input-files"]], "Install ETE v4": [[0, "install-ete-v4"]], "Install TreeProfiler": [[0, "install-treeprofiler"]], "Installation": [[0, "installation"]], "Interactive visualization interface": [[0, "interactive-visualization-interface"]], "Introduction": [[0, "introduction"]], "Lable Layout": [[0, "lable-layout"]], "Layouts for Analytical Data": [[0, "layouts-for-analytical-data"]], "Layouts for Multiple Sequence Alignment": [[0, "layouts-for-multiple-sequence-alignment"]], "Layouts for Numerical data": [[0, "layouts-for-numerical-data"]], "Layouts for Taxonomy annotation": [[0, "layouts-for-taxonomy-annotation"]], "Layouts for boolean data": [[0, "layouts-for-boolean-data"]], "Layouts for categorical data": [[0, "layouts-for-categorical-data"]], "Layouts for eggnog-mapper functional annotations": [[0, "layouts-for-eggnog-mapper-functional-annotations"]], "Layouts for eggnog-mapper pfam/smart annotations": [[0, "layouts-for-eggnog-mapper-pfam-smart-annotations"]], "Lineage Specificity Layout": [[0, "lineage-specificity-layout"]], "Lineage specificity analysis": [[0, "lineage-specificity-analysis"]], "Manual installation": [[0, "manual-installation"]], "Metadata TSV/CSV as a numerical data matrix": [[0, "metadata-tsv-csv-as-a-numerical-data-matrix"]], "Metadata without column names": [[0, "metadata-without-column-names"]], "Missing value detection": [[0, "missing-value-detection"]], "Numerical Matrix Layout": [[0, "numerical-matrix-layout"]], "Output formats for annotated trees": [[0, "output-formats-for-annotated-trees"]], "Phylogenetic signal delta statistic": [[0, "phylogenetic-signal-delta-statistic"]], "Piechart Layout": [[0, "piechart-layout"]], "Profiling Layout": [[0, "profiling-layout"]], "Query Syntax": [[0, "query-syntax"]], "Query in internal nodes": [[0, "query-in-internal-nodes"]], "Quick Start with examples dataset": [[0, "quick-start-with-examples-dataset"]], "Quick install via pip": [[0, "quick-install-via-pip"]], "Reading input tree": [[0, "reading-input-tree"]], "Rectangle Layout": [[0, "rectangle-layout"]], "Setting color range for numerical data": [[0, "setting-color-range-for-numerical-data"]], "Specifying data types for metadata columns": [[0, "specifying-data-types-for-metadata-columns"]], "Table of Contents": [[0, "table-of-contents"]], "TaxonClade Layout": [[0, "taxonclade-layout"]], "TaxonCollapse Layout": [[0, "taxoncollapse-layout"]], "TaxonRectangle Layout": [[0, "taxonrectangle-layout"]], "Taxonomic annotation": [[0, "taxonomic-annotation"]], "Tree format": [[0, "tree-format"]], "Tree parser": [[0, "tree-parser"]], "TreeProfiler Tutorial": [[0, null]], "Unmapped tree leaf property detection": [[0, "unmapped-tree-leaf-property-detection"]], "Use standard input and output formats": [[0, "use-standard-input-and-output-formats"]], "Using TreeProfiler": [[0, "using-treeprofiler"]], "Using different taxonomic databases from GTDB/NCBI": [[0, "using-different-taxonomic-databases-from-gtdb-ncbi"]], "Welcome to treeprofiler\u2019s documentation!": [[1, null]], "Wildcard settings of color range for numerical matrix": [[0, "wildcard-settings-of-color-range-for-numerical-matrix"]], "emapper annotation output and the summary method": [[0, "id3"]], "treeprofiler-annotate computing phylogenetic profiles and annotation": [[0, "treeprofiler-annotate-computing-phylogenetic-profiles-and-annotation"]], "treeprofiler-plot visualizing phylogenetic profiles and annotation": [[0, "treeprofiler-plot-visualizing-phylogenetic-profiles-and-annotation"]]}, "docnames": ["documentations", "index"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["documentations.rst", "index.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": 0, "0": 0, "000": 0, "0000003": 0, "0000902": 0, "0000904": 0, "00018867741670758483": 0, "0002164578877048098": 0, "0002801019197914036": 0, "0003006": 0, "0003094673156738281": 0, "00043984526187224396": 0, "00048506476303705997": 0, "00048818236055906636": 0, "0005949760547048478": 0, "001": 0, "001324183303131325": 0, "00151915289715353": 0, "0019142742715016286": 0, "001965821926394849": 0, "001968860626220703": 0, "0034043477773810613": 0, "0056147812629824085": 0, "008000": 0, "00czay4286": 0, "00seay5240": 0, "01": 0, "011256165797407233": 0, "013434856612985015": 0, "015213913144468159": 0, "0195194146220156e": 0, "023102310231023": 0, "0244": 0, "027189256680401872": 0, "028430041000376213": 0, "036044144428": 0, "036556538": 0, "039125443": 0, "04825388395749479": 0, "04976016557186095": 0, "05": 0, "05160331726074219": 0, "05933033400048369": 0, "06": 0, "0632016": 0, "065917563705425": 0, "07": 0, "0732456957024559e": 0, "08034": 0, "09": 0, "098": 0, "0ustar": 0, "1": 0, "10": 0, "100": 0, "10000": 0, "10020": 0, "10090": 0, "115": 0, "115599899": 0, "117": 0, "117570": 0, "117571": 0, "117741186968884e": 0, "118": 0, "12": 0, "120": 0, "122": 0, "123": 0, "12655333321138568": 0, "127": 0, "128": 0, "13": 0, "130889": 0, "131": 0, "131567": 0, "1338369": 0, "138": 0, "138062": 0, "14": 0, "1437010": 0, "152tax": 0, "152tax_annot": 0, "15g": 0, "16": 0, "160049964146": 0, "166914": 0, "169266432": 0, "17363108674806": 0, "175": 0, "186": 0, "188666": 0, "188681": 0, "19": 0, "190563": 0, "194": 0, "1969": 0, "1970": 0, "1981": 0, "1987": 0, "1997": 0, "2": 0, "20": 0, "200": 0, "2000": 0, "2003": 0, "200px": 0, "2014": 0, "202": 0, "2023": 0, "207": 0, "207598": 0, "214": 0, "2172": 0, "2173": 0, "2174": 0, "2175": 0, "219065": 0, "22": 0, "220": 0, "220000": 0, "23": 0, "24": 0, "245": 0, "248282": 0, "26": 0, "261": 0, "27": 0, "272": 0, "2759": 0, "276": 0, "28": 0, "29": 0, "2978723404255319": 0, "3": 0, "31": 0, "3100000000000005": 0, "3121192529798287": 0, "313833": 0, "314146": 0, "314293": 0, "314295": 0, "315846": 0, "318": 0, "32": 0, "3244296265415": 0, "32523": 0, "32524": 0, "32525": 0, "326": 0, "3276816717486982": 0, "33": 0, "33154": 0, "33208": 0, "33213": 0, "335": 0, "33511": 0, "349": 0, "35": 0, "356": 0, "362": 0, "366": 0, "375390078": 0, "376913": 0, "38": 0, "39": 0, "4": 0, "40": 0, "40674": 0, "41": 0, "42": 0, "43": 0, "44": 0, "443782202699844": 0, "447": 0, "45": 0, "45303222603186877": 0, "458423": 0, "458698485629717e": 0, "46": 0, "463526916666666": 0, "471596": 0, "47894": 0, "479": 0, "49": 0, "494": 0, "5": 0, "50": 0, "5000": 0, "509": 0, "50px": 0, "51": 0, "5156064132880938": 0, "5196": 0, "52": 0, "52340888828994": 0, "524138873540599": 0, "526654599": 0, "52779174042388": 0, "5384554640742852": 0, "56": 0, "585": 0, "591": 0, "6": 0, "60": 0, "6072": 0, "63": 0, "64": 0, "6552": 0, "667": 0, "67": 0, "671": 0, "676": 0, "683": 0, "684109": 0, "69": 0, "692277320371426": 0, "6g": 0, "7": 0, "70": 0, "713": 0, "73": 0, "73449420928955": 0, "746": 0, "74908423423767": 0, "767844": 0, "76837158203125e": 0, "7711": 0, "7739": 0, "7740000000000002": 0, "7742": 0, "7776": 0, "7817176831389784": 0, "79": 0, "792161": 0, "8": 0, "805286": 0, "815704818": 0, "825": 0, "8287": 0, "86": 0, "8620000000000001": 0, "87": 0, "870000000000001": 0, "871": 0, "89": 0, "89593": 0, "898": 0, "9": 0, "90365": 0, "906460531980665": 0, "92825": 0, "9347": 0, "937": 0, "9384942099527859": 0, "9443": 0, "9462054466377042": 0, "947": 0, "9473989345272481": 0, "9497450729621073": 0, "94cyaf6237": 0, "95": 0, "9526": 0, "9598": 0, "96": 0, "9604": 0, "9605": 0, "9606": 0, "96060539505257": 0, "96cmaj6134": 0, "97": 0, "97338": 0, "9752818930521312": 0, "97cdaf6238": 0, "97cdaf6240": 0, "9801547427961053": 0, "98cmaj6932": 0, "98cmaj6933": 0, "99": 0, "9937640783202009": 0, "9999517018762923": 0, "A": 0, "And": 0, "As": 0, "At": 0, "But": 0, "By": 0, "For": 0, "If": 0, "In": 0, "It": 0, "Or": 0, "Such": 0, "The": 0, "Then": 0, "To": 0, "With": 0, "_annot": 0, "_annotated_prop2typ": 0, "_avg": 0, "_counter": 0, "_demo": 0, "_f1": 0, "_max": 0, "_min": 0, "_prec": 0, "_sen": 0, "_std": 0, "_sum": 0, "abl": 0, "about": 0, "abov": 0, "abs_data": 0, "abs_data2": 0, "absenc": 0, "absolut": 0, "acceler": 0, "accept": 0, "access": 0, "accord": 0, "account": 0, "accpept": 0, "acctran": 0, "accumul": 0, "accur": 0, "acr_continuous_column": 0, "acr_continuous_layout": 0, "acr_discrete_column": 0, "acr_discrete_layout": 0, "across": 0, "action": 0, "activ": 0, "ad": 0, "adapt": 0, "add": 0, "adjust": 0, "adopt": 0, "aesara": 0, "africa": 0, "after": 0, "against": 0, "ahli": 0, "ahlicontain": 0, "aim": 0, "al": 0, "alayoni": 0, "albania": 0, "albanian": 0, "alfaroi": 0, "algorithm": 0, "align": 1, "alinig": 0, "all": 0, "allisoni": 0, "allow": 0, "aln": 0, "along": 0, "alongsid": 0, "alreadi": 0, "also": 0, "altern": 0, "although": 0, "ambigu": 0, "amniota": 0, "among": 0, "an": 0, "analyt": 1, "analytic_exampl": 0, "analyz": 0, "ancestor": 0, "ani": 0, "annot": 1, "annotate_taxa": 0, "anntot": 0, "anoli": 0, "anolis_annot": 0, "anoth": 0, "apart": 0, "app": 0, "appear": 0, "appil": 0, "appli": 0, "approach": 0, "approxim": 0, "aquatic_habitat": 0, "ar": 0, "ar122_metadata_r202": 0, "ar122_metadata_r202_lit": 0, "archaea": 0, "archaea_annot": 0, "archaeal": 0, "archiv": 0, "argument": 0, "arrai": 0, "array_avg": 0, "array_max": 0, "array_min": 0, "array_std": 0, "array_sum": 0, "assign": 0, "associ": 0, "attach": 0, "auto": 0, "automat": 0, "automatic_queri": 0, "avail": 0, "averag": 0, "avg": 0, "awk": 0, "b": 0, "bac120_metadata_r202": 0, "bac120_metadata_r202_lit": 0, "background_layout": 0, "bacteri": 0, "bacteria": 0, "bar": 0, "barplot_layout": 0, "base": 1, "basic": 1, "basic_example0": 0, "basic_example1": 0, "basic_example1_annot": 0, "basic_example1_metadata1": 0, "basic_example1_metadata2": 0, "basic_example1_prop2typ": 0, "basic_example2": 0, "bayesian": 0, "becaus": 0, "becom": 0, "befor": 0, "being": 0, "below": 0, "besid": 0, "between": 0, "bigg_react": 0, "bilateria": 0, "billion": 0, "bin": 0, "binary_aggregate_layout": 0, "binary_layout": 0, "binary_matrix_layout": 0, "binary_unicolor_aggregate_layout": 0, "binary_unicolor_layout": 0, "biolog": 0, "biopython": 0, "black": 0, "blob": 0, "block": 0, "blue": 0, "bm": 0, "bool": 0, "bool_prop": 0, "bool_prop_idx": 0, "bool_properti": 0, "bool_property_count": 0, "bool_typ": 0, "bool_type2": 0, "boolean": 1, "boreoeutheria": 0, "both": 1, "bottl": 0, "bottom": 0, "branch": 0, "brier": 0, "brite": 0, "brotli": 0, "brownian": 0, "bubble_layout": 0, "build": 0, "burn": 0, "button": 0, "c": 0, "c__heimdallarchaeia": 0, "c__korarchaeia": 0, "calcul": 0, "call": 0, "can": 1, "cantor": 0, "capac": 0, "case": 0, "cat": 0, "catarrhini": 0, "categor": 1, "categorci": 0, "categorical1": 0, "categorical1_count": 0, "categorical_dupl": 0, "categorical_matrix_layout": 0, "caus": 0, "cazi": 0, "cd": 0, "cellular": 0, "certain": 0, "chang": 0, "character_": 0, "character_countri": 0, "check": 0, "children": 0, "choos": 1, "chordata": 0, "circl": 0, "circular": 0, "circumst": 0, "clade": 0, "class": 0, "classif": 0, "clone": 0, "close": 0, "cluster": 0, "code": 0, "cog_categori": 0, "col": 0, "col1": 0, "col1_avg": 0, "col1_max": 0, "col1_min": 0, "col1_std": 0, "col1_sum": 0, "col2": 0, "col2_avg": 0, "col3": 0, "col4": 0, "col5": 0, "col6": 0, "collapse_demo": 0, "color": 1, "color_config": 0, "color_max": 0, "color_mid": 0, "color_min": 0, "color_nan": 0, "colorbi": 0, "colorbranch_layout": 0, "column_summary_method": 0, "columnnam": 0, "com": 0, "comman": 0, "command": 0, "commen": 0, "common_nam": 0, "compar": 0, "comparison": 0, "compgenomicslab": 0, "complet": 0, "composit": 0, "compress": 0, "comput": 1, "conda": 0, "condit": 1, "conditinari": 0, "conduct": 0, "config": 1, "config_sep": 0, "configur": 0, "consensu": 0, "consesu": 0, "consid": 0, "consist": 0, "conson": 0, "construct": 0, "consult": 0, "contain": 0, "context": 0, "control": 0, "convert": 0, "copi": 0, "corner": 0, "correct": 0, "correctli": 0, "correspon": 0, "correspond": 0, "could": 0, "count": 0, "counter": 0, "countri": 0, "country_count": 0, "country_delta": 0, "country_pv": 0, "cover": 0, "cpu": 0, "craniata": 0, "creat": 0, "criteria": 0, "criterion": 0, "cross": 0, "cryptofilum": 0, "ctg": 0, "ctrl": 0, "current": 0, "cusom": 0, "cusomt": 0, "custom": 1, "custom_color": 0, "customdb": 0, "cut": 0, "cutoff": 0, "cython": 0, "d": 0, "d__archaea": 0, "data": 1, "data_2col": 0, "data_dir": 0, "data_matrix": 0, "datamatrix": 0, "dataset": 1, "datat": 0, "datatyp": 0, "db": 0, "de": 0, "debug": 0, "decid": 0, "decorate_gff": 0, "default": 0, "defin": 0, "degre": 0, "delai": 0, "delimit": 0, "deltran": 0, "demo": 0, "demo1": 1, "demo1_annot": 0, "demo1_prop2typ": 0, "demo2": 1, "demo2_annot": 0, "demo2_l": 0, "demo3": 0, "demo3_annot": 0, "demo4": 0, "demonstr": 0, "demostr": 0, "dengdenggtdb_genome_repres": 0, "dengzq1234": 0, "denovo": 0, "depend": 1, "dependeci": 0, "deploy": 0, "describ": 0, "descript": 0, "design": 0, "desir": 0, "despit": 0, "detail": 0, "detech": 0, "determin": 0, "deuterostomia": 0, "dev": 0, "develop": 0, "deviat": 0, "diamond": 0, "differen": 0, "dipnotetrapodomorpha": 0, "directli": 0, "directori": 0, "discret": 0, "disk": 0, "displai": 0, "dist": 0, "distanc": 0, "dmnd_algo": 0, "dmnd_ignore_warn": 0, "do": 0, "doe": 0, "doesn": 0, "done": 0, "dont": 0, "down": 0, "download": 0, "downpass": 0, "draw_arrai": 0, "due": 0, "dump": 0, "dynam": 0, "e": 0, "each": 0, "easi": 0, "easili": 0, "easteurop": 0, "ec": 0, "ecogenom": 0, "editor": 0, "effect": 0, "effici": 0, "eft": 0, "eggnog": 1, "eggnog5": 0, "eggnog6": 0, "eggnog_og": 0, "either": 0, "electron": 0, "emapper_annot": 0, "emapper_demo": 0, "emapper_job": 0, "emapper_layout": 0, "emapper_pfam": 0, "emapper_smart": 0, "emapper_web_job": 0, "embed": 0, "embl": 0, "empti": 0, "enabl": 0, "encount": 0, "end": 0, "ensdorp00000023664": 0, "ent": 0, "entir": 0, "entropi": 0, "env": 0, "environ": 0, "ephrin_rec_lik": 0, "equal": 0, "equilibrium": 0, "error": 0, "estim": 0, "et": 1, "etc": 0, "ete4": 0, "etetoolkit": 0, "euarchontoglir": 0, "eukaryota": 0, "eumetazoa": 0, "euteleostomi": 0, "eutheria": 0, "evalu": 0, "even": 0, "everi": 0, "evolbioinfo": 0, "evoltyp": 0, "evolut": 0, "evolutionari": 0, "exact": 0, "exampl": 1, "example1": 0, "example1_demo": 0, "example2_demo": 0, "excel": 0, "execut": 0, "expect": 0, "experiment": 0, "explor": 1, "express": 0, "extract": 0, "f": 0, "f1": 0, "f81": 0, "f__kariarchaeacea": 0, "f__korarchaeacea": 0, "faa": 0, "facilit": 0, "fact": 0, "falp": 0, "fals": 0, "famili": 0, "farri": 0, "fast": 0, "fasta": 0, "featur": 0, "feb": 0, "felsenstein": 0, "few": 0, "figur": 0, "figure1_al": 0, "file": 1, "filenam": 0, "filetyp": 0, "fill": 0, "find": 0, "fine": 0, "first": 0, "fit": 0, "fix": 0, "flag": 0, "flask": 0, "flexibl": 0, "float": 0, "focus": 0, "follow": 0, "forc": 0, "forg": 0, "forget": 0, "forkserv": 0, "format": 1, "former": 0, "formula": 0, "found": 0, "framework": 0, "frequenc": 0, "ftp": 0, "full": 0, "fullam": 0, "fullfil": 0, "function": 1, "g": 0, "g__korarchaeum": 0, "g__lc": 0, "gascuel": 0, "gb_gca_003344655": 0, "gb_gca_011358815": 0, "gb_gca_014116815": 0, "gc_percentag": 0, "gcc": 0, "gcc_linux": 0, "gene": 1, "gener": 0, "genom": 0, "genome_s": 0, "genu": 0, "gini": 0, "git": 0, "github": 0, "given": 0, "glanc": 0, "global": 0, "gnathostomata": 0, "go": 0, "go_evid": 0, "gov": 0, "gradient": 0, "grain": 0, "graphic": 0, "greater": 0, "greec": 0, "green": 0, "grei": 0, "group": 0, "gtdb": 1, "gtdb202dump": 0, "gtdb_demo": 0, "gtdb_id": 0, "gtdb_latest_dump": 0, "gtdb_r202": 0, "gtdb_taxid": 0, "gtdb_taxonomi": 0, "gtdb_v202": 0, "gtdb_v202_annot": 0, "gtdblatest": 0, "gtdbv202": 0, "gtdbv202_annot": 0, "gtdbv202full_demo": 0, "gtdbv202lite_demo": 0, "guaranti": 0, "gui": 0, "gz": 0, "ha": 0, "habitat": 1, "handi": 0, "haplorrhini": 0, "have": 0, "head": 0, "header": 0, "heatmap_layout": 0, "heatmap_mean_layout": 0, "heatmap_zscore_layout": 0, "heidelberg": 0, "help": 0, "henc": 0, "here": 0, "hex": 0, "high": 0, "highest": 0, "highli": 0, "highlight_demo": 0, "histori": 0, "hit": 0, "hky": 0, "hmmfrom": 0, "hmmto": 0, "home": 0, "hominida": 0, "hominina": 0, "hominoidea": 0, "homo": 0, "hope": 0, "horizont": 0, "host_associ": 0, "how": 0, "howev": 0, "http": 0, "huge": 0, "i": 0, "id": 0, "idx": 0, "illustr": 0, "implement": 0, "importantli": 0, "improv": 0, "impur": 0, "includ": 0, "incompat": 0, "inconsist": 0, "independ": 0, "index": [0, 1], "indic": 0, "individu": 0, "induc": 0, "infer": 0, "inform": 1, "infraord": 0, "input": 1, "input_tre": 0, "inrectli": 0, "instal": 1, "instead": 0, "int": 0, "integ": 0, "integr": 0, "interact": 1, "interfac": 1, "intern": 1, "internal_c": 0, "internal_nod": 0, "internal_pars": 0, "introduct": 1, "iron": 0, "is_albania": 0, "is_greec": 0, "iter": 0, "its": 0, "itwil": 0, "ityp": 0, "j": 0, "jc": 0, "joint": 0, "jtt": 0, "juke": 0, "just": 0, "keep": 0, "kegg": 0, "kegg_ko": 0, "kegg_modul": 0, "kegg_pathwai": 0, "kegg_rclass": 0, "kegg_react": 0, "kegg_tc": 0, "kei": 0, "kept": 0, "kind": 0, "kingdom": 0, "ko": 0, "l": 0, "label": 0, "label_layout": 0, "lambda0": 0, "larg": 1, "latest": 0, "latestest": 0, "latter": 0, "launch": 0, "layout": 1, "lazi": 0, "lca": 0, "leaf_a": 0, "leaf_nam": 0, "leafnam": 0, "least": 0, "leav": 0, "left": 0, "left_valu": 0, "legend": 0, "length": 0, "less": 0, "let": 0, "letter": 0, "level": 1, "librari": 0, "lightweight": 0, "like": 0, "likelihood": 0, "limit": 1, "line": 0, "linear": 0, "link": 0, "linux": 0, "list": 0, "list_data": 0, "load": 0, "load_metadata_to_tre": 0, "local": 0, "localhost": 0, "locat": 0, "log": 0, "log_likelihood": 0, "log_likelihood_restricted_joint": 0, "log_likelihood_restricted_map": 0, "log_likelihood_restricted_mppa": 0, "loos": 0, "low": 0, "ls_column": 0, "ls_layout": 0, "lse": 0, "m": 0, "maddison": 0, "mage_n": 0, "mai": 0, "main": 0, "mainli": 0, "make": 0, "mammalia": 0, "manual": 1, "map": 0, "mapper": 1, "margin": 0, "marginal_prob": 0, "marker": 0, "massiv": 0, "matplotlib": 0, "matter": 0, "max": 0, "max_annot_lvl": 0, "maximum": 0, "mean": 0, "measur": 0, "medium": 0, "meet": 0, "memori": 0, "mention": 0, "merg": 0, "merge_gtdbtre": 0, "metadata": 1, "metadata_sep": 0, "metadata_tab": 0, "metadata_tab_l": 0, "metazoa": 0, "method": 1, "method_": 0, "method_mppa": 0, "metric": 1, "metrix": 0, "middl": 0, "might": 0, "min": 0, "miniconda3": 0, "minim": 0, "minimap": 0, "minimu": 0, "minimum": 0, "minut": 0, "missing_gtdb_v202": 0, "missing_gtdb_v202_annot": 0, "missing_ncbi": 0, "ml": 0, "mm_knn6rw6j": 0, "mode": 0, "model": 0, "model_": 0, "model_f81": 0, "modul": [0, 1], "moment": 0, "mon": 0, "more": 0, "most": 0, "motion": 0, "mp": 0, "mp_start_method": 0, "mppa": 0, "multipl": 1, "multiple_text_prop": 0, "multiple_text_properti": 0, "multiple_text_property_count": 0, "must": 0, "mutat": 0, "mute": 0, "n": 0, "n3": 0, "n4": 0, "n7": 0, "named_lineag": 0, "namespac": 0, "nan": 0, "natur": 0, "navig": 0, "ncbi_annot": 0, "ncbi_assembly_level": 0, "ncbi_demo": 0, "ncbi_genome_categori": 0, "ncbi_id": 0, "need": 0, "neg": 0, "nei": 0, "new": 0, "newick": 0, "next": 0, "nhx": 0, "nifh": 1, "nifh_annot": 0, "nih": 0, "nitrogenas": 0, "nlm": 0, "node": 1, "node_1": 0, "node_2": 0, "node_3": 0, "node_4": 0, "node_5": 0, "non": 0, "none": 0, "normal": 0, "note": 0, "notic": 0, "novel": 0, "now": 0, "null": 0, "num": 0, "num_prop": 0, "num_prop_idx": 0, "num_scenario": 0, "num_serv": 0, "num_states_per_node_avg": 0, "num_unresolved_nod": 0, "number": 0, "numer": 1, "numerical2": 0, "numerical3": 0, "numerical_matrix_layout": 0, "numerical_properti": 0, "numerical_property_avg": 0, "numerical_property_max": 0, "numerical_property_sum": 0, "numpi": 0, "nw": 0, "nwk": 0, "o": 0, "o__korarchaeal": 0, "o__uba460": 0, "obtain": 0, "off": 0, "onc": 0, "one": 0, "onli": 0, "oper": 0, "opisthokonta": 0, "optim": 0, "optimis": 0, "option": 1, "order": 0, "org": 0, "organ": 0, "ornstein": 0, "ortholog": 0, "orthologi": 0, "other": 0, "otherwis": 0, "ou": 0, "ouput": 0, "our": 0, "out": 0, "outdir": 0, "output": 1, "output_dir": 0, "overrid": 0, "overview": 0, "own": 0, "p": 0, "p__asgardarchaeota": 0, "p__thermoproteota": 0, "p_val": 0, "p_valu": 0, "packag": 0, "pad": 0, "page": 1, "panel": 0, "parallel": 0, "param": 0, "paramet": 0, "pars": 0, "parse_csv": 0, "parser": 1, "parsimoni": 0, "part": 0, "partial": 0, "parvord": 0, "pass": 0, "pastml": 0, "pastml2ete4": 0, "pastml_vers": 0, "path": 0, "per": 0, "percentag": 0, "percis": 0, "perform": 0, "pfam": 1, "pfam_realign": 0, "phy003i7zj_chick": 0, "phy004o1e0_aptfo": 0, "phy004pa1b_anapl": 0, "phy004tlna_apavi": 0, "phy00508fr_nipni": 0, "phy0054bo3_melga": 0, "phylogenei": 0, "phylogenet": 1, "phylogeni": 0, "phylum": 0, "phylumn": 0, "pident": 0, "piechart_layout": 0, "piechartfac": 0, "pip": 1, "pipelin": 0, "plain": 0, "platform": 0, "pleas": 0, "plot": 1, "plu": 0, "png": 0, "posit": 0, "possibl": 0, "posterior": 0, "posteriori": 0, "pratic": 0, "pratical_exampl": 0, "pre": 0, "prec": 0, "prec_cutoff": 0, "precis": 0, "precomput": 0, "predefin": 0, "predict": 0, "preferred_nam": 0, "prepar": 0, "presenc": 0, "present": 0, "preset": 0, "press": 0, "previou": 0, "primat": 0, "print": 0, "priorit": 0, "prioritis": 0, "probabilist": 0, "probabl": 0, "process": 0, "produc": 0, "product": 0, "profil": 1, "profile1": 0, "profile1_count": 0, "profile1_f1": 0, "profile1_prec": 0, "profile1_sen": 0, "profiling_layout": 0, "progenome3": 1, "progenome_demo": 0, "progenomes3": 0, "program": 0, "prokaryot": 0, "prop": 0, "prop1": 0, "prop2": 0, "prop2typ": 0, "prop2type_fil": 0, "prop_nam": 0, "propab": 0, "propabl": 0, "proper": 0, "properli": 0, "propertii": 0, "property_nam": 0, "proport": 0, "protein": 0, "protein_count": 0, "provid": 0, "prthologi": 0, "prune_demo": 0, "ptn": 0, "pub": 0, "pupko": 0, "put": 0, "px": 0, "py": 0, "pymc": 0, "pyqt": 0, "python": 0, "q": 0, "queri": 1, "query_cov": 0, "query_coverag": 0, "query_length": 0, "query_nam": 0, "quick": 1, "quiet": 0, "quit": 0, "r": 0, "ram": 0, "random_column1": 0, "random_column1_avg": 0, "random_column1_max": 0, "random_column1_min": 0, "random_column1_std": 0, "random_column1_sum": 0, "random_column2": 0, "random_column2_avg": 0, "random_column3": 0, "random_column3_avg": 0, "random_column3_sum": 0, "random_typ": 0, "random_type_count": 0, "rank": 0, "rank_limit": 0, "rate": 0, "ratio": 0, "raw": 0, "read": 1, "real": 0, "reccomend": 0, "receiv": 0, "recfac": 0, "recommend": 0, "recov": 0, "rectangle_layout": 0, "rectangular": 0, "rectfac": 0, "red": 0, "reduc": 0, "refer": 0, "reflect": 0, "regardless": 0, "reinstal": 0, "rel": 0, "relat": 0, "relationship": 0, "releas": 0, "release202": 0, "reli": 0, "rememb": 0, "remov": 0, "render": 0, "replac": 0, "repo": 0, "report_ortholog": 0, "repositori": 0, "repres": 0, "represent": 0, "requir": 0, "rerun": 0, "resolv": 0, "resourc": 0, "respect": 0, "result": 0, "resum": 0, "return": 0, "revers": 0, "right": 0, "right_valu": 0, "root": 0, "row": 0, "rs_gcf_000019605": 0, "rs_gcf_000730245": 0, "rs_gcf_001560035": 0, "rs_gcf_003948265": 0, "rs_gcf_004210275": 0, "run": 0, "s__korarchaeum": 0, "s__lc": 0, "salmon": 0, "same": 0, "sample1": 0, "sample1_avg": 0, "sample2": 0, "sample3": 0, "sample4": 0, "sample5": 0, "sapien": 0, "sarat": 0, "sarcopterygii": 0, "scale": 0, "scan": 0, "scenario": 0, "sci_nam": 0, "scipi": 0, "score": 0, "script": 0, "se": 0, "search": [0, 1], "second": 0, "see": 0, "seed_ortholog": 0, "select": 0, "selenium": 0, "sen": 0, "sens_cutoff": 0, "sensit": 0, "sep": 0, "separ": 0, "seper": 0, "seqfrom": 0, "seqto": 0, "sequenc": 1, "seri": 0, "serv": 0, "server": 0, "session": 0, "setup": 0, "sh": 0, "shannon": 0, "share": 0, "shm": 0, "short": 0, "should": 0, "show": 0, "show_tree_prop": 0, "shown": 0, "signific": 0, "simiiform": 0, "similar": 0, "simpli": 0, "singl": 0, "situat": 0, "size": 0, "smaller": 0, "smart": 1, "smartview": 0, "so": 0, "softwar": 0, "soil_habitat": 0, "solut": 0, "solv": 0, "some": 0, "sometim": 0, "sourc": 0, "sp001940725": 0, "space": 0, "speci": 0, "special": 0, "ss": 0, "stack": 0, "standpoint": 0, "start": 1, "stat": 0, "state": 0, "std": 0, "stdout": 0, "steel": 0, "step": 0, "still": 0, "store": 0, "str": 0, "strategi": 0, "string": 0, "structur": 0, "sub": 0, "subcommand": 0, "subfamili": 0, "subject_cov": 0, "subord": 0, "subphylum": 0, "subset": 0, "subspeci": 0, "subtre": 0, "successfulli": 0, "sucessfulli": 0, "suffix": 0, "suitabl": 0, "sum": 0, "sum_scor": 0, "summar": 0, "summur": 0, "superclass": 0, "superfamili": 0, "superkingdom": 0, "superord": 0, "support": 0, "svl": 0, "switch": 0, "swofford": 0, "symbol": 0, "syntax": 1, "t": 0, "tab": 0, "table1": 0, "table2": 0, "take": 0, "tar": 0, "target": 0, "target_ortholog": 0, "tax_scop": 0, "taxa": 0, "taxa_0": 0, "taxa_1": 0, "taxa_2": 0, "taxa_3": 0, "taxa_4": 0, "taxa_dump": 0, "taxa_field": 0, "taxadb": 0, "taxadump": 0, "taxdump": 0, "taxid": 0, "taxon_column": 0, "taxon_delimit": 0, "taxonom": 1, "taxonomi": 1, "taxonomy_exampl": 0, "tbd": 0, "teleostomi": 0, "tell": 0, "temp_dir": 0, "templat": 0, "term": 0, "termin": 0, "test": 0, "tetrapoda": 0, "text": 0, "text_prop": 0, "text_prop_idx": 0, "text_properti": 0, "text_property_count": 0, "textfac": 0, "than": 0, "thei": 0, "them": 0, "theoret": 0, "therefor": 0, "theria": 0, "thi": 0, "thin": 0, "those": 0, "thread": 0, "three": 0, "threshold": 0, "time": 0, "tip": 0, "titl": 0, "togeth": 0, "tool": 0, "toolkit": 0, "top": 0, "total": 0, "trace": 0, "transfer": 0, "transform": 0, "trati": 0, "travers": 0, "tre": 0, "treat": 0, "tree": 1, "tree_annot": 0, "treeprofielr": 0, "treeprofiler_galleri": 0, "true": 0, "try": 0, "tsv0000664000175000017500000343216414447266674012351": 0, "turn": 0, "tutori": 1, "two": 0, "txt": 0, "typic": 0, "u": 0, "uhlenbeck": 0, "unannot": 0, "uncertain": 0, "under": 0, "uniqu": 0, "univers": 0, "unknown": 0, "up": 0, "updat": 0, "us": 1, "usag": 1, "user": 0, "user_data": 0, "v202": 0, "v4": 1, "val": 0, "variabl": 0, "variou": 0, "veri": 0, "version": 0, "vertebrata": 0, "vertic": 0, "via": 1, "view": 0, "violat": 0, "visual": 1, "visualis": 0, "visul": 0, "vowel": 0, "w": 0, "wa": 0, "wai": 0, "want": 0, "warn": 0, "we": 0, "westeurop": 0, "wget": 0, "when": 0, "where": 0, "which": 0, "while": 0, "white": 0, "whole": 0, "whose": 0, "width": 0, "within": 0, "won": 0, "word": 0, "work": 0, "would": 0, "wsgi": 0, "wt": 0, "www": 0, "x": 0, "xf": 0, "xfam": 0, "xp_002609184": 0, "xth": 0, "y": 0, "ye": 0, "yellow": 0, "you": 0, "your": 0, "z": 0, "zcat": 0, "zero": 0, "zhang": 0, "zip": 0, "zoom": 0, "zscore": 0}, "titles": ["TreeProfiler Tutorial", "Welcome to treeprofiler\u2019s documentation!"], "titleterms": {"": 1, "AND": 0, "OR": 0, "acr": 0, "advanc": 0, "aggreg": 0, "align": 0, "analysi": 0, "analyt": 0, "ancestr": 0, "annot": 0, "background": 0, "barplot": 0, "base": 0, "basic": 0, "binari": 0, "boolean": 0, "both": 0, "bubbl": 0, "can": 0, "categor": 0, "charact": 0, "choos": 0, "collaps": 0, "color": 0, "colorbranch": 0, "column": 0, "combin": 0, "complex": 0, "comput": 0, "condit": 0, "config": 0, "content": [0, 1], "continu": 0, "contiun": 0, "csv": 0, "custom": 0, "data": 0, "databas": 0, "dataset": 0, "delta": 0, "demo1": 0, "demo2": 0, "depend": 0, "detect": 0, "differ": 0, "document": 1, "domain": 0, "duplic": 0, "eggnog": 0, "emapp": 0, "et": 0, "exampl": 0, "explor": 0, "field": 0, "file": 0, "format": 0, "from": 0, "function": 0, "gene": 0, "gtdb": 0, "habitat": 0, "handl": 0, "heatmap": 0, "highlight": 0, "identifi": 0, "ignor": 0, "indic": 1, "inform": 0, "input": 0, "instal": 0, "interact": 0, "interfac": 0, "intern": 0, "introduct": 0, "labl": 0, "larg": 0, "layout": 0, "leaf": 0, "level": 0, "limit": 0, "lineag": 0, "manual": 0, "mapper": 0, "matrix": 0, "metadata": 0, "method": 0, "metric": 0, "miss": 0, "msa": 0, "multipl": 0, "name": 0, "ncbi": 0, "nifh": 0, "node": 0, "numer": 0, "option": 0, "output": 0, "parser": 0, "pfam": 0, "phylogenet": 0, "piechart": 0, "pip": 0, "plot": 0, "profil": 0, "progenome3": 0, "properti": 0, "prune": 0, "queri": 0, "quick": 0, "rang": 0, "read": 0, "reconstruct": 0, "rectangl": 0, "sequenc": 0, "set": 0, "signal": 0, "smart": 0, "specif": 0, "specifi": 0, "standard": 0, "start": 0, "statist": 0, "summari": 0, "syntax": 0, "tabl": [0, 1], "taxon": 0, "taxonclad": 0, "taxoncollaps": 0, "taxonom": 0, "taxonomi": 0, "taxonrectangl": 0, "trait": 0, "tree": 0, "treeprofil": [0, 1], "tsv": 0, "tutori": 0, "type": 0, "unclassifi": 0, "unicolor": 0, "unmap": 0, "us": 0, "usag": 0, "v4": 0, "valu": 0, "via": 0, "visual": 0, "welcom": 1, "wildcard": 0, "without": 0}})
\ No newline at end of file