Phylogenetics Documentation

This documentation will provide information and guidelines about how we use the Phylogenetics modules related to this package.


Phylogenetics is best defined as the study of evolutionary relationships among biological entities. In our case, those entities are species. We are seeking to learn how mammals (more specifically primates) compare to each other given a group of genes (GPCRs and addiction related).

PAML in particular is the most rigorous software for helping us to understand the potentially significant differences in genes across different mammalian species. From there, we can decide which genes we will further study in cell culture projects or assays.


It is critical to have these phylogenetic software installed and avalailable on your path in order to use the Phylogenetics submodules or you can take a look at our external apps repository to help you install these software on your machine.

Modules/Attributes available

from OrthoEvol.Orthologs import Phylogenetics

# Find out what subclasses are available for use



In the beginning stages of our project, we tested various phylogenetic programs to see which worked well for us.

In this module, we include classes and ways to use PAML, Phylip, PhyML, IQTREE, and Biopython’s Bio.Phylo class.

Using PhyML with RelaxPhylip

# Now you can import a class you want to utilize
from OrthoEvol.Orthologs.Phylogenetics import PhyML, RelaxPhylip

RelaxPhylip("HTR1A_aligned.fasta", "HTR1A_aligned.phy")

# Generate a maximum likelihood tree from the phylip formatted alignment file.

View detailed PhyML documentation.


from OrthoEvol.Orthologs.Phylogenetics.PAML import ETE3PAML

paml = ETE3PAML(alignmentfile='.ffn', speciestree='.nw', workdir='')'path/to/codeml/binary', output_folder=None)

View detailed PAML documentation.

Using the FilteredTree implementation of IQTree

from OrthoEvol.Orthologs.Phylogenetics import FilteredTree

FilteredTree(alignment, dataType='CODON', working_dir='path/of/working/directory')

View detailed IQTree documentation.