PAML Documentation

PAML (Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood and is maintained by Ziheng Yang.

Why ETE?

ETE is python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

Model Selection and Default Parameters

It’s important to note the default parameters for ETE3PAML are as follows: model='M1', `workdir=```.

Usage & Examples

A simple implementation of ETE3PAML

from OrthoEvol.Orthologs.Phylogenetics.PAML import ETE3PAML

paml = ETE3PAML(alignmentfile='.ffn', speciestree='.nw', workdir='')

paml.run(pamlsrc='path/to/codeml/binary', output_folder=None)

Pruning a tree for use with ETE3PAML

from OrthoEvol.Orthologs.Phylogenetics.PAML import ETE3PAML

paml = ETE3PAML(alignmentfile='HTR1A.ffn', speciestree='speciestree.nw', workdir='')

# Input a list of orgnanisms or an organisms csv file with header as 'Organisms'
paml.prune_tree(organisms='organisms.csv')

paml.run(pamlsrc='path/to/codeml/binary', output_folder=None)