smot: a python package and CLI tool for contextual phylogenetic subsampling

Abstract

smot (Simple Manipulation Of Trees) is a command line tool and Python package with the pragmatic goal of distilling large-scale phylogenetic data to facilitate visualization without jeopardizing inference. This package offers subsampling algorithms that preserve reference taxa and tree topology, algorithms for classifying unlabeled tips given a subset of labeled reference tips, and functions for filtering phylogenetic trees. The smot tool has broad application in phylogenetic analysis and we demonstrate its utility using a genomic epidemiology study of influenza A virus in swine.