phylosophy is an R toolkit for generating and exploring complex phylogenetic profiles. It provides solutions for searching orthologs for a set of genes of interest, enhancing the functional linkages between query genes and their orthologs with feature similarity scores, and finally visually exploring the phylogenetic profiles of query genes.
phylosophy requires R (version ≥ 4.0). Please install or update R on your computer before continue.
Some components of phylosophy also requires Python (version ≥ 3.0). Make sure you have python3 to use all functions of phylosophy.
phylosophy can be installed as same as other R packages using devtools library. Start R and use these command lines to install the tool
if (!requireNamespace("devtools"))
install.packages("devtools")
devtools::install_github("BIONF/phylosophy", INSTALL_opts = c('--no-lock'), build_vignettes = TRUE)
Besides, some components of DCC require an additional installation. Please follow their instruction.
phylosophy is a modular program, i.e. each component/function has it own module and can run independently from each other. Not all the inside apps can be installed automatically with phylosophy. If you wish to use all apps, you need to install some of them by yourself.
Normally, when you start phylosophy in the same environment where you installed those tools, no further action required. However, if you are working with RStudio, probably you have already known that RStudio's environment configuration could be different than the one of bash/zsh. In this case, you need to put the following lines to your ~/.Rprofile file to make phylosophy works:
# path config for python3
Sys.setenv(PATH = paste("/path/to/your/Python/3.7/bin", Sys.getenv("PATH"), sep=":"))
# path config for HaMStR-oneSeq
Sys.setenv(PATH = paste("/path/to/your/HaMStR/bin", Sys.getenv("PATH"), sep=":"))
# path config for annoFAS (a function of greedyFAS)
Sys.setenv(COILSDIR = "/path/to/your/annotation_fas/COILS2/coils")
From the R terminal, enter:
library(phylosophy)
runPhylosophy()Check your web browser, phylosophy will be displayed there ;-)
phylosophy contains the following apps:
- MILTS:
- BUSCO: Assessing gene set completeness
- DCCv2: Compiling core sets for HaMStR
- FAS: Calculating pairwise protein feature architecture similarity
- HaMStR: Searching feature-aware orthologs
- PhyloProfile: Exploring complex phylogenetic profiles
blablabla
[NAME] is an R package for assessing the completenss of a given gene set. Similar to BUSCO, [NAME] compares the user input gene set with its pre-calculated hierarchical core ortholog data and assign those core genes if they are present, missing or different in term of functional equivalence.
[NAME] can be used as a independent tool (install from its github page) or as an app included in phylosophy (no installation required).
DCCv2 is a tool for compiling core set data for HaMStR using predicted orthologs from OMA, both OMA-browser and OMA-standalone. Outputs of this tool are 3 (optional 4) folders required for a HaMStR run, including (1) core_orthologs (comprises of OMA orthologous group - OG, or OMA pairs - OP. Each OG/OP has its own directory, where a multiple fasta file and a corresponding profile HMM can be found), (2) genome_dir (contains gene sets of taxa, from which the orthologs are originated), (3) blast_dir (holds the blast databases of those gene sets within genome_dir), and an optional (4) weight_dir (contains feature architecure annotations of all gene sets).
For OMA-standalone, DCCv2 requires the output orthoXML file from OMA, a taxon mapping file in tab-delimited format containing 3 columns (blabla) (blabla) (blabla). Protein set of included taxa can be either given as a folder, or automatically downloaded from OMA database.
To use DCCv2 with OMA-browser, some data from OMA need to be downloaded and processed in advance using the function Get OMA data under the DCCv2 menu of phylosophy. For OMA-browser, DCCv2 accept input as NCBI taxonomy IDs, taxon names or an OMA group ID. If only 2 taxa are given, one can decided if OMA groups or OMA pairs should be taken into account.
DCCv2 is delivered together with phylosophy. No additional installation needed.
greedyFAS is a python tool for calculating the so called FAS-score, which is a measure of how similar the feature architectures of two proteins are.
greedyFAS (version ≥ 1.2.0) needs to be installed for using the FAS app and the complete function of HaMStR app. Please follow the instruction on its github site for more information.
FAS app contains 2 main functions. One is used only for doing feature annotation for a multiple FASTA input. This function gets use of the annoFAS function of greedyFAS. The second one performs the architecture similarity calculation, which is done by the calcFAS function.
HaMStR-oneSeq is a advanced version of HaMStR (Ebersberger et al. 2009), an feature-aware orthology search tool.
Similar to greedyFAS, HaMStR-oneSeq needs to be manually installed using this manual.
HaMStR-oneSeq comes with a pre-calculated data set containing the default 78 taxa of the Quest for Ortholog consortium. A new taxon can be added to HaMStR-oneSeq, if it follows the naming schema of HaMStR-oneSeq and has some additional information such as the annotated features and its blast database. HaMStR app provides a function to simplify this process. One needs only submit the FASTA file of the species of interest and its taxon ID (can be the NCBI taxonomy, but it is not a must).
PhyloProfile is an R package for integrating, visualizing and exploring complexed phylogenetic profile (Tran et al. 2018).
In phylosophy, there are 2 versions of PhyloProfile. For a quick visualizing and basic filtering of the phylogenetic profiles, a lite version of PhyloProfile has been directly implemented inside phylosophy. For utilize the complete functions of that package, a tab in phylosophy will open the full version of PhyloProfile's GUI tool.
PhyloProfile will be automatically installed together with phylosophy. However, if you are using PhyloProfile for the first time, you need to start the full version once to getting the required taxonomy data, even when you only need the lite version.
Vinh Tran [email protected]