PhyKIT

PhyKIT is a command-line toolkit for processing and analyzing multiple sequence alignments, phylogenetic trees, and comparative trait data.

Start here

First analysis

Install PhyKIT with Python 3.10 or newer, download the example alignment, and calculate its length:

python -m pip install phykit
curl -LO https://jlsteenwyk.github.io/PhyKIT/data/Steenwyk_etal_mBio_2019_EOG091N44MS.aln.fa
phykit alignment_length Steenwyk_etal_mBio_2019_EOG091N44MS.aln.fa

Expected output:

The value is the number of aligned sites. Continue with Tutorial 1 to measure additional information-content and tree-quality statistics.

Citation

If you use PhyKIT, cite PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data, Bioinformatics, doi:10.1093/bioinformatics/btab096.