An easy to use and comprehensive package which aids in the analysis and visualization of comparative genomics & related bioinformatics projects. This package places emphasis on the inference of orthologs using NCBI's blast, aligning sequences, and phylogenetics analyses including PAML, PhymL, ete3, and more tools.
The goal of this project was to create a simple, short, & effective pipeline (refseq accession to phyloanalysis) to infer orthologs.
Check out our wiki docs and our read the docs!
pip install Datasnakes-Scripts
Alternatively, you can set install the package manually.
- Download the zip file and unzip it or
git clone https://github.com/datasnakes/Datasnakes-Scripts.git cd Datasnakes-Scriptspip install .
from Datasnakes.Orthologs import Align, BioSQL, Blast, CompGenetics, Phylogenetics, GenbankTo run tests, type nosetests Tests/ in the Datasnakes-Orthologs directory.
- Rob Gilmore | Github: @grabear | 📧
- Shaurita Hutchins | Github: @sdhutchins | Twitter: @MavenNBA | 📧
If you would like to contribute to this package, install the package in development mode, and check out our `contributing guidelines <>`_.
git clone http://github.com/datasnakes/Datasnakes-Scriptscd Datasnakes-Scriptspip install -e .
We're so thankful to have a resource such as Biopython. They inspired this package.
Cock, P.J.A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878