PartitionFinder

Description

PartitionFinder is free open source software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses. Most of the lab's coding output currently goes into PartitionFinder.

License

GNU General Public licence version 3.

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 partitionfinder and load default version of partitionfinder as

module avail partitionfinder/ # list available modules
module load partitionfinder   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail partitionfinder

and choose explicit version you want to use. Then run as

$ PartitionFinder.py

You can run the application by typing PartitionFinder.py instead of python PartitionFinder.py which is used in the manual. To see other parameters of PartitionFinder type PartitionFinder.py --help. In the same manner you can run choooseK.py. If you would like to run distruct.py you have to use graphical environment. To work with graphical application you can run command module add gui followed by the command gui start). More information about the remote desktop you can find at https://wiki.metacentrum.cz/wiki/Remote_desktop

Documentation

Manuál 1.1.1 and http://www.robertlanfear.com/partitionfinder/tutorial/

Homepage

URL: http://www.robertlanfear.com/partitionfinder URL: https://github.com/roblanf/partitionfinder