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 dataype is 'aa' (amino acid), but you may use ‘nt’ for nuclueotide.

Examples

Running Phyml

from OrthoEvol.Orthologs.Phylogenetics.PAML import ETE3PAML

PhyML(phyml_input='path/to/phylip/multisequencealignment', datatype='aa')

Running Phyml with our parallel module

from OrthoEvol.Orthologs.Phylogenetics.PAML import ETE3PAML

PhyML(phyml_input='path/to/phylip/multisequencealignment', datatype='aa')

Notes

This class is designed PhyML version 3.1.