PhyML Documentation

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing Nearest Neighbor Interchanges (NNIs) to improve a reasonable starting tree topology.

Learn more about PhyML here.

Default Parameters

The default datatype is 'aa' (amino acid), but you may use ‘nt’ for nucleotide.

Examples

Running Phyml

from OrthoEvol.Orthologs.Phylogenetics.PhyML import PhyML

htr1a = PhyML(infile='HTR1A.phy', datatype='aa')
htr1a.run()

Running Phyml with our parallel module

from OrthoEvol.Orthologs.Phylogenetics.PhyML import PhyML
from OrthoEvol.Tools.parallel import Multiprocess

files = ['HTR1A.phy', 'HTR1E.phy', 'MAOA.phy']

def phyml(filename):
    phyml = PhyML(infile=filename, datatype='aa')
    phyml.run()

if __name__ == '__main__':
    mp = Multiprocess()
    mp.map2function(phyml, files)

Notes

This class is designed for PhyML version 3.1.