GeneRax is a parallel tool for species tree-aware maximum likelihood based gene family tree inference under gene duplication, transfer, and loss.
It infers gene family trees from their aligned sequences, the mapping between genes and species, and a rooted undated species tree. In addition, it infers the duplication, transfer and loss events that best (in terms of maximum likelihood) reconcile the gene family trees with the species trees.
It accounts for sequence substitutions, gene duplication, gene loss and horizontal gene transfer.
When using GeneRax, please cite: https://academic.oup.com/mbe/article/doi/10.1093/molbev/msaa141/5851843
GeneRax is also available on bioconda
SpeciesRax is part of the GeneRax tool and is available since GeneRax v2.0.0. SpeciesRax infers a rooted species tree from a set of unrooted gene trees. When using SpeciesRax, please cite https://academic.oup.com/mbe/article/39/2/msab365/6503503
Update: we have released a new tool AleRax (paper) which an independent study (preprint) has shown to be more accurate than SpeciesRax and other competing methods for species tree inference.
(If you are not installing with bioconda)
- A Linux or MacOS environnement
- gcc 5.0 or >
- CMake 3.6 or >
- MPI
(Please note that you can also install through bioconda)
To download GeneRax, please use git, and clone with --recursive!!!
git clone --recursive https://github.com/BenoitMorel/GeneRax
To build the sources:
./install.sh
See the wiki (https://github.com/BenoitMorel/GeneRax/wiki)
For questions, issues or feedback, please post on our google group: https://groups.google.com/g/generaxusers When reporting an issue, please send us at least the command line you ran, the logs file and the families file. The more information we get, the quicker we can solve the problems :-)