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README.md

GeneRax

GeneRax is a parallel tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss.

It infers gene trees from their aligned sequences, the mapping between genes and species, and a rooted undated species tree.

It accounts for sequence substitutions, gene duplication, gene loss and horizontal gene transfer.

Preprint: https://www.biorxiv.org/content/biorxiv/early/2019/09/26/779066.full.pdf

GeneRax is also available on bioconda

Requirement

(If you are not installing with bioconda)

  • A Linux or MacOS environnement
  • gcc 5.0 or >
  • CMake 3.6 or >
  • MPI
  • bison and flex parsers

Installation

(Please note that you can also install through bioconda)

Installing the dependencies on Ubuntu and other Debian-based systems:

sudo apt-get install flex bison libgmp3-dev

On other systems: GNU Bison Flex GMP

To download GeneRax, please use git, and clone with --recursive!!!

git clone --recursive https://github.com/BenoitMorel/GeneRax

To build the sources:

./install.sh

Running

See the wiki (https://github.com/BenoitMorel/GeneRax/wiki)

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