Information about software packages installed on the ICHEC systems.
P4 is a Python package that does maximum likelihood and Bayesian phylogenetic analyses on molecular sequences. It's specialty is that you can use heterogeneous models, where the model parameters can differ in different parts of the tree, or over different parts of the data. P4 was written by Peter G. Foster, The Natural History Museum, London.
p4 is distributed under the GPL
To use p4, load the relevant environment module "p4", along with the module "numpy-gnu" which p4 is dependent upon:
Further information can be obtained from http://www.bmnh.org/web_users/pf/p4.html
How to cite p4:
Foster P.G. (2004)
Modeling compositional heterogeneity.
Systematic Biology53: 485-495.