Installation and first analysis

Requirements

PhyKIT supports Python 3.10, 3.11, 3.12, and 3.13. Use a virtual environment to keep its dependencies separate from other projects.

Install from PyPI

python -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install phykit
phykit version

On Windows PowerShell, activate the environment with .venv\Scripts\Activate.ps1.

Install with conda

conda create -n phykit -c conda-forge -c bioconda phykit
conda activate phykit
phykit version

Run a first analysis

Create a working directory and download a versioned example alignment.

mkdir phykit-first-analysis
cd phykit-first-analysis
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:

624

PhyKIT read an aligned FASTA file and reported its 624 aligned sites. Request structured output with --json:

phykit alignment_length Steenwyk_etal_mBio_2019_EOG091N44MS.aln.fa --json

Find the next command

• Alignment quality and composition: Alignment quality and statistics

• Tree summaries: Tree summary statistics

• Tree comparison: Tree comparison and consensus

• Trait evolution: Trait evolution

• Comparative methods: Phylogenetic comparative methods

• Introgression and gene flow: Introgression and gene flow

For any command, display the interface installed in the active environment:

phykit <command> --help