ParGenes
A massively parallel tool for model selection and tree inference on thousands of genes
Features
ParGenes is a parallel tool that takes as input a set of multiple sequence alignments (typically from different genes) and infers their corresponding phylogenetic trees.
ParGenes supports the following features:
- best-fit model selection with ModelTest
- phylogenetic tree inference with RAxML-NG (with customizable number of starting trees and bootstrap trees)
- automatic parallelization to make the best use of the available computing cores
- checkpointing: ParGenes can be restarted without effort after an interuption
- error reporting for the MSAs that fail to be treated
- options to customize the tree inference parameters
- optional call to ASTRAL to infer a species tree from the inferred phylogenetic trees
Requirement
- Linux or MacOS
- gcc 5.0 or >
- CMake 3.6 or >
- Either MPI or OpenMP. MPI for multiple nodes parallelization (clusters).
Installation
(Please note that, on linux, you can also install through bioconda)
Please use git, and clone with --recursive!!!
git clone --recursive https://github.com/BenoitMorel/ParGenes.git
To build the sources:
./install.sh
To parallelize the compilation with 10 cores:
./install.sh 10
Updating the repository
Instead of using:
git pull
please use:
./gitpull.sh
Rational: we use git submodule, and git pull might not be enough to update all the changes. The gitpull.sh will update all the changes properly.
Running
See the wiki (https://github.com/BenoitMorel/ParGenes/wiki/Running-ParGenes)
Documentation and Support
Documentation: in the github wiki.
Also please check the online help with python3 pargenes/pargenes.py --help
A suggestion, a bug to report, a question? Please use the RAxML google group.
Citing
Before citing ParGenes, please make sure you read https://github.com/BenoitMorel/ParGenes/wiki/Citation