Orthologs Documentation

This top level module includes submodules such as Align (for aligning multi fasta files), Phylogenetics (for analyzing multiple sequence alignments), `BioSQL <>`__ (for database creation), Blast (includes tools for using NCBI’s blastn command line), and Genbank. (for tools to extract features from genbank files).

Usage & Examples

These classes are optimized to be used together (very little work to do that), but can also be used as standalone classes/methods.

This is a simple example of using all of the Orthologs submodules together.

from OrthoEvol.Orthologs.Blast import OrthoBlastN
from OrthoEvol.Orthologs.Align import ClustalO
from OrthoEvol.Orthologs.Phlogenetics import ETE3PAML

Software Dependencies

Ensure that the following software is installed and in your path: Clustal omega, NCBI Blast+ 2.6.0 or greater, PAML, PhyML, Phylip, IQTREE, Mafft, Prank, Clustalw, Guidance2 & Pal2Nal

If you are a sudo user, you may use the script we’ve provided, install.sh.

Using install.sh on Debian/Ubuntu:

# Change to the directory of the file.
chmod +x install.sh

View Readmes for Orthologs Modules

  • OrthoEvol.Orthologs.Align - Align documentation.
  • OrthoEvol.Orthologs.GenBank - GenBank documentation.
  • OrthoEvol.Orthologs.Blast - Blast documentation.
  • OrthoEvol.Orthologs.Phylogenetics - Phylogenetics documentation.