Phyparts

Description

This module allows executing PhyParts and PhyParts PieCharts.

PhyParts is meant to examine clades from a set of trees that may include duplications and incomplete taxon sampling. This is often the case with transcriptomes and genomes. These are relatively simple mapping analyses, intended to allow for exploration of large datasets.

PhyParts PieCharts is a script for generating piecharts on a phylogeny that has run through PhyParts.

License

Public

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 phyparts and load default version of phyparts as

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

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

module avail phyparts

and choose explicit version you want to use.

phyparts # runs the phyparts analysis
phypartspiecharts # runs the phypartspiecharts.py script to plot pie charts on the species phylogeny showing the percentage of concordant gene trees, percentage in the top alternative bipartition, other conflicting topologies, and uninformative genes.

Documentation

https://bitbucket.org/blackrim/phyparts/src/master/README.md https://github.com/mossmatters/phyloscripts/tree/master/phypartspiecharts

Homepage

https://bitbucket.org/blackrim/phyparts/src/master/README.md https://github.com/mossmatters/phyloscripts/tree/master/phypartspiecharts