Welcome to ShotgunUnifrac’s documentation!

ShotgunUnifrac is a snakemake pipeline for generating a consensus phylogeny over many species. It can either create a phylogeny per core gene over a selection of genomes and then combining them together or it can append core genes directly into a super-alignment. The pipeline is written in snakemake and includes a python library for data curation and prep. View the Quickstart Guide page to see a worked example of installing and using the pipeline.