Phycas

Description

Phycas is a Python application for carrying out phylogenetic analyses. Phycas is also a C++ and Python library that can be used to create new applications or to extend the current functionality.

License

GNU GPL v2, see http://www.gnu.org/licenses/gpl-2.0.html for details.

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 phycas and load default version of phycas as

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

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

module avail phycas

and choose explicit version you want to use. After initialization is available a program binary phycas. Just run

phycas

to enter the Phycas shell. Logout can be done via ctrl-d shortcut.

Documentation

Documentation is available at http://phylo.bio.ku.edu/phycas/manual.pdf or in /software/phycas-1.2.0/phycas/docs directory. Some examples are in the Phycas installation directory at /software/phycas-1.2.0/phycas/phycas/Examples.

Homepage

http://hydrodictyon.eeb.uconn.edu/projects/phycas/index.php/Phycas_Home