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.