PhySpeTree: automatically reconstructing phylogenetic species tree

Documents: PhySpeTree documentation.

• Introduction
• PhySpeTree workflow
• Features
• Install
• Usage
  • autobuild
    • autobuild options
    • Advance options
  • build
    • build options
    • Advance options
  • combine
    • combine options
  • iview
    • iview options
  • check
    • check options
• Frequently Asked Questions (FAQ)
  • PhySpeTree input/output
  • PhySpeTree reconstruct phylogenetic tree database

Introduction

Understanding phylogenetic relationships between different species is crucial for evolutionary studies. Reconstructing the phylogenetic species tree, a branching diagram, is particularly useful in inferring evolutionary relationships. For example, the tree-of-life provides a remarkable view of organizing principles of the biological world. So, the exact species tree to be reconstructed is necessary, but the process of reconstructing the species or gene tree is very tedious.

Here, we developed an easy-to-use package named PhySpeTree that is convenient to reconstruct species trees by one command line. Two independent pipelines were included by using the most adopted small subunit ribosomal RNA (SSU rRNA) and concatenated highly conserved proteins (HCP), respectively. A distinct advantage is that users only need to input species names and PhySpeTree automatically downloads and analyzes sequences of SSU rRNA or HCP from about 4,000 organisms.

PhySpeTree workflow

PhySpeTree workflow includes the following steps:

1. Prepare organisms names (abbreviated name) to reconstruct species tree as example.
2. Two parallel pipelines to reconstruct species tree (SSU rRNA (--sran) or highly conserved proteins (--hcp)).
3. Querying, parsing and retrieving FASTA format data.
4. Multiple sequence alignment by Muscle or ClustalW.
5. Concatenate highly conserved proteins by PhySpeTree.
6. Select conserved blocks by Gblosks.
7. Reconstruct species tree by RAxML or FastTree.
8. Output the reconstruct phylogenetic tree files.

Features

• Easy to use (one command line automatically reconstruct species tree).
• Multi-selection (select reconstruct species tree by HCP method or SSU rRNA method).
• Adjustable parameters (the users can choice any enable parameters with corresponding invoke software).
• Provide species names (species abbreviated names) as input only.
• Combine best phylogenetic tree (combine multiple tree to a consensus tree).
• View tree by iTol (easily use iview module to annotate tree).
• Flexible (more software to be invoked with corresponding enable parameters).
• Versatile software (can build species tree or gene tree and also ability extend new species to tree).

Install

1. PhySpeTree is released on PyPI, so all you need install:

$ pip install PhySpeTree

To upgrade to latest version:

$ pip install --upgrade PhySpeTree

2. Download PhySpeTree released version form PypI:

• Download PhySpeTree by PypI latest released version
• local installation:

$ pip install PhySpeTree-*.tar.gz

3. You can install PhySpeTree by downloading the latest released version form github:

• Download latest released version .tar.gz file.
• Local installation:

$ pip install physpetools-v*.tar.gz

4. Use the git command clone PhySpeTree to install it:

$ git clone [email protected]:xiaofeiyangyang/physpetools.git

$ cd physpetools

$ python setup.py install

Usage

autobuild

Users should prepare a TXT file contain the species names (abbreviated names) example.

Use autobuild in command line like this:

$ PhySpeTree -i organism_example_list.txt [options]*

autobuild options

-h	Print help message and exits.
-i	Input a TXT file contain the species names (abbreviated names) are same with KEGG species abbreviation.
-o	A directory include output data (tree files). The default output data name is Outdata.
-t	Specify the number of processing threads (CPUs) to reconstruct phylogenetic tree. The default is 1.
--hcp	Specify the hcp (highly conserved protein) method to reconstruct phylogenetic tree. The default method is hcp.
--ehcp	The ehcp mode is use highly conserved proteins with extend highly conserved protein (users provide) to reconstruct phylogenetic tree.
--srna	The srna (SSU rRNA) method is use SSU rRNA data to reconstruct phylogenetic tree.
--esrna	The esrna mode is use SSU RNA sequence with extend SSU RNA sequence (users provide) to reconstruct phylogenetic tree.

Advance options

Users enable choice more detail options with PhySpeTree call software, detail advance options input must be enclosed in single quotes and Start with a space.

The following is an example of using RAxML advanced options:

$ PhySpeTree -i organism_example_list.txt --raxml --raxml_p '-f a -m GTRGAMMA  -p 12345 -x 12345 -# 100 -n T1'

--muscle	Multiple sequence alignment by muscle. The default multiple sequence alignment software is Muscle.
--muscle_p	Set Muscle advance parameters. The default is -maxiter 100. More options about Muscle please to see MUSCLE Manual. -maxiter maximum number of iterations to run is set 100.
--clustalw	Multiple sequence alignment by clustalw2.
--clustalw_p	Set clustalw2 advance parameters. Here use clustalw default parameters. More options about clustalw please to see Clustalw Help.
--gblocks	Set Gblocks advance parameters. The default is -t=p -e=-gb1. More options about Gblocks please to see Gblocks documentation. -t Choice type of sequence. PhySpeTree default set is protein. -e Generic File Extension. PhySpeTree set default is -gbl1.
--raxml	Reconstruct phylogenetic tree by RAxML. The default build tree software is RAxML.
--raxml_p	Set reconstruct phylogenetic tree arguments with RAxML. The default is -f a -m PROTGAMMAJTTX -p 12345 -x 12345 -# 100 -n T1. More options about RAxMl please to see RAxML Manual. -f select algorithm. The PhySpeTree default set is a, rapid Bootstrap analysis and search for best­scoring ML tree in one program run. -m Model of Binary (Morphological), Nucleotide, Multi­State, or Amino Acid Substitution. The PhySpeTree default set is PROTGAMMAJTTX. -p Specify a random number seed for the parsimony inferences. The physep default set is 12345. -x Specify an integer number (random seed) and turn on rapid bootstrapping. The PhySpeTree default set is 12345. -N The same with -# specify the number of alternative runs on distinct starting trees. The PhySpeTree default set is 100.
--fasttree	Reconstruct phylogenetic tree by FastTree.
--fasttree_p	Set FastTree advance parameters. More options about FastTree please to see FastTree.

build

Users can reconstruct phylogenetic tree use build module by manually prepared files. such as, SSU rRNA sequence or highly conserved proteins.

Use build in command line to reconstruct phylogenetic tree:

• build phylogenetic tree by highly conserved proteins method:

$ PhySpeTree build -i example_hcp -o output --hcp

• build phylogenetic tree by SSU rRNA sequence method:

$ PhySpeTree build -i example_16s_ssurna.fasta -o output --sran

build options

-h	Print help message and exits.
-i	Input a TXT file contain the species names (abbreviated names) are same with KEGG species abbreviation.
-o	A directory include output data (tree files). The default output data name is Outdata.
-t	Specify the number of processing threads (CPUs) to reconstruct phylogenetic tree. The default is 1.
--hcp	Specify the hcp (highly conserved protein) method to reconstruct phylogenetic tree. The default method is hcp.
--srna	The srna (SSU rRNA) method is use SSU rRNA data to reconstruct phylogenetic tree.

Advance options

Users enable choice more detail options with PhySpeTree call software, detail advance options input must be enclosed in single quotes and start with space.

The following is an example of using RAxML advanced options:

$ PhySpeTree -i organism_example_list.txt --raxml --raxml_p ' -f a -m GTRGAMMA  -p 12345 -x 12345 -# 100 -n T1'

--muscle	Multiple sequence alignment by muscle. The default multiple sequence alignment software is Muscle.
--muscle_p	Set Muscle advance parameters. The default is -maxiter 100. More options about Muscle please to see MUSCLE Manual. -maxiter maximum number of iterations to run is set 100.
--clustalw	Multiple sequence alignment by clustalw2.
--clustalw_p	Set clustalw2 advance parameters. Here use clustalw2 default parameters. More options about clustalw2 please to see Clustalw Help.
--gblocks	Set Gblocks advance parameters. The default is -t=p -e=-gb1. More options about Gblocks please to see Gblocks documentation. -t Choice type of sequence. PhySpeTree default set is protein. -e Generic File Extension. PhySpeTree set default is -gbl1.
--raxml	Reconstruct phylogenetic tree by RAxML. The default build tree software is RAxML.
--raxml_p	Set reconstruct phylogenetic tree arguments with RAxML. The default is -f a -m PROTGAMMAJTTX -p 12345 -x 12345 -# 100 -n T1. More options about RAxMl please to see RAxML Manual. -f select algorithm. The PhySpeTree default set is a, rapid Bootstrap analysis and search for best­scoring ML tree in one program run. -m Model of Binary (Morphological), Nucleotide, Multi­State, or Amino Acid Substitution. The PhySpeTree default set is PROTGAMMAJTTX. -p Specify a random number seed for the parsimony inferences. The physep default set is 12345. -x Specify an integer number (random seed) and turn on rapid bootstrapping. The PhySpeTree default set is 12345. -N The same with -# specify the number of alternative runs on distinct starting trees. The PhySpeTree default set is 100.
--fasttree	Reconstruct phylogenetic tree by FastTree.
--fasttree_p	Set FastTree advance parameters. More options about FastTree please to see FastTree.

combine

The combine module for the consensus tree construction.

In Linux you can easy combine more tree to a tree file, for example:

$ cat tree1.tree tree2.tree > combineTree.tree

Use combine in command line like this:

$ PhySpeTree PhySpeTree combine -i combineTree.tree [options]*

combine options

-h	Print help message and exits.
-i	Input a tree file (PHYLIP format), which contain multiple tree.
-o	A directory contain combined tree file. The default output data name is combineTree.
--mr	Compute majority rule consensus tree.
--mre	Compute extended majority rule consensus tree.
--strict	Compute strict consensus tree.

iview

Users can Annotating tree by iview module by iTol.

Use iview in command line like this:

$ PhySpeTree iview -i organism_example_list.txt --range

iview options

-h	Print help message and exits.
-i	Input a TXT file contain species names (abbreviated names) are same with KEGG species abbreviation.
-o	A directory contain the generate configure files. The directory name is iview.
-r	Annotating ranges by kingdom, phylum, class or order. The default is phylum.
-a	Colored ranges by users assign, users can choice from [kingdom, phylum, class and order].
-l	Change species labels from abbreviated names to full names.

check

The check module design for check input organisms whether match in KEGG database or SILVA database.

$ PhySpeTree check -i organism_example_list.txt -out check --ehcp

check options

-h	Print help message and exits.
-i	Input a TXT file contain species names (abbreviated names) are same with KEGG species abbreviation.
-o	A directory contain check result. The default directory name is check.
--hcp	Check organisms whether supported by KEGG database.
--ehcp	check input organisms prepare for extend autobuild tree module.
--srna	Check organisms whether supported by SILVA database.

Frequently Asked Questions (FAQ)

PhySpeTree input/output

1.What preparation of users should does for PhySpeTree?

The users should prepare a TXT file, which contain species name (abbreviated names are same with KEGG database.), one line write one species name only. For example, organism_example_list. You can retrieve the Abbreviation of species names by KEGG API.

2.What's PhySpeTree output data mean?

PhySpeTree output two data files, the one is a result file default names is Outdata, another is a temp file.

If you reconstruct phylogenetic tree by --hcp (highly conserved protein) method, the temp file sinclude three directory: conserved_protein, muscle_alignment and concatenate.

• conserved_protein: Store the FASTA format files, which was highly conserved proteins retrieved from KEGG database.
• alignment: Store the sequence files has been aligned.
• concatenate: Include concatenated highly conserved proteins data (FASTA format) and selected conserved blocks data (*.fasta-gb1 format file).

If you reconstruct phylogenetic tree by --srna (SSU rRNA) method, the temp files include two directory: rna_sequence and rna_alignment.

• rna_sequence: Store a file named rna_sequence.fasta, contain the SSU rRNA sequence retrieved from SILVA database.
• ran_alignment: Store in the *.fasta file is the sequence files has been aligned and the *.fasta-gb1, *fasta-gb1.html are select conserved blocks data (use Gblocks software), the *.phy format file is converted from select conserved blocks data by PhySpeTree.

NOTE:

Users can check the quality of every aspect of data by the corresponding temp files.

PhySpeTree reconstruct phylogenetic tree database

what's the highly conserved proteins be used to reconstruct phylogenetic tree?

PhySpeTree use 31 highly conserved proteins to reconstruct phylogenetic tree. This highly conserved proteins exclusion Horizontal Gene Transfers (HGTs) already.

cite:

Ciccarelli F D, Doerks T, Von Mering C, et al. Toward automatic reconstruction of a highly resolved tree of life[J]. science, 2006, 311(5765): 1283-1287.

The 31 highly conserved proteins and corresponding KEGG database KO number as follow table:

Protein Names	Eukaryotes KO	Prokaryotes KO
DNA-directed RNA polymerase subunit alpha	K03040	K03040
Ribosomal protein L1	K02865	K02863
Leucyl-tRNA synthetase	K01869	K01869
Metal-dependent proteases with chaperone activity	K01409	K01409
Phenylalanine-tRNA synthethase alpha subunit	K01889	K01889
Predicted GTPase probable translation factor	K06942	K06942
Preprotein translocase subunit SecY	K10956	K10956
Ribosomal protein L11	K02868	K02867
Ribosomal protein L13	K02873	K02871
Ribosomal protein L14	K02875	K02874
Ribosomal protein L15	K02877	K17437
Ribosomal protein L16/L10E	K02866	K02872
Ribosomal protein L18	K02883	K02882
Ribosomal protein L22	K02891	K02890
Ribosomal protein L3	K02925	K02906
Ribosomal protein L5	K02932	K02931
Ribosomal protein L6P/L9E	K02940	K02939
Ribosomal protein S11	K02949	K02948
Ribosomal protein S15P/S13E	K02958	K02956
Ribosomal protein S17	K02962	K02961
Ribosomal protein S2	K02981	K02967
Ribosomal protein S3	K02985	K02982
Ribosomal protein S4	K02987	K02986
Ribosomal protein S5	K02989	K02988
Ribosomal protein S7	K02993	K02992
Ribosomal protein S8	K02995	K02994
Ribosomal protein S9	K02997	K02996
Seryl-tRNA synthetase	K01875	K01875
Arginyl-tRNA synthetase	K01887	K01887
DNA-directed RNA polymerase beta subunit	K03043	K03043
Ribosomal protein S13	K02953	K02952

2.How the SSU rRAN database was created?

The SSU rRAN database was created by SILVA SSU rRNA database project (version: SILVA SSU 123.1 release). In this data the sequences haven been truncated, which means that all nucleotides that have not been aligned were removed from the sequence.