# p4_bygene_compotest.py v1.0 # # Chris Laumer 3 April 2014 GPL v2 # # This is a minimally written script, designed to individually test a set of genes # for compositional heterogeneity using null simulations as implemented in p4 v0.9.0, # simulating on inferred ML gene trees. Run it in a folder for which you have, with # each gene, the following information: # # a.) A phylip-formatted MSA, named [gene].phylip # b.) A maximum likelihood tree in newick form, here called RAxML_bestTree.[gene]_ML # c.) A model, in the format output by ProteinModelSelection.pl, named [gene]_model.txt. # The only models supported are those used by p4; you may have to modify ProteinModelSelection.pl # accordingly. # # If these conditions are met, running the script should print the name of each gene, plus # the p-value for the null test, both to standard output and to a file called "by_gene_compo_test.txt". # If you are running it on a computer with many CPUs, the python multiprocessing module # will automatically try to use all of those processes (good for an HPC cluster, bad for a desktop).