Guenomu
Description
Guenomu means "genome" in Japanese, and is a software written in C that estimates the species tree for a given set of gene families. Theoretically it will work with aligned sequences, one alignment per gene family, but at the moment it is functional only if you provide the distribution of gene trees for each family. That is, you must provide it with the possible gene topologies for each gene family, and the program will sample species trees compatible with these gene trees assuming that the disagreement between them is a composition between duplication and losses, deep coalescences, or other stochastic processes.
License
GNU GPLv2
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of guenomu and load default version of guenomu as
module avail guenomu/ # list available modules module load guenomu # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail guenomu
and choose explicit version you want to use.
For MPI version (mpi module is automatically added by guenomu module) eg.
mpirun -np 2 guenomu run_importance_sampling.ctrl
Documentation
https://bitbucket.org/leomrtns/guenomu/wiki/Home#!how-to-run