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-NG
• 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
• check pointing: ParGenes can be restarted without effort after an interruption
• error reporting for the MSAs that fail to be treated
• options to customize the tree inference parameters
• optional call to ASTRAL or ASTER to infer a species tree from the inferred phylogenetic trees

Requirements

• 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 submodules, 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.