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.
GeneRax is also available on
(If you are not installing with bioconda)
- A Linux or MacOS environnement
- gcc 5.0 or >
- CMake 3.6 or >
- bison and flex parsers
(Please note that you can also install through
Installing the dependencies on Ubuntu and other Debian-based systems:
sudo apt-get install flex bison libgmp3-dev
To download GeneRax, please use git, and clone with --recursive!!!
git clone --recursive https://github.com/BenoitMorel/GeneRax
To build the sources:
See the wiki (https://github.com/BenoitMorel/GeneRax/wiki)