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.
cd
chmod +x install.sh
./sudo-install.sh