Phytest: quality control for phylogenetic analyses

Abstract

Motivation: The ability to automatically conduct quality control checks on phylogenetic analyses is becoming more important with the increase in genetic sequencing and the use of real-time pipelines e.g. in the SARS-CoV-2 era. Implementations of real-time phylogenetic analyses require automated testing to make sure that problems in the data are caught automatically within analysis pipelines and in a timely manner. Here, we present Phytest (version 1.1) a tool for automating quality control checks on sequences, trees and metadata during phylogenetic analyses. Results: Phytest is a phylogenetic analysis testing program that easily integrates into existing phylogenetic pipelines. We demonstrate the utility of Phytest with real-world examples. Availability and implementation: Phytest source code is available on GitHub (https://github.com/phytest-devs/phyt est) and can be installed via PyPI with the command ‘pip install phytest’. Extensive documentation can be found at https://phytest-devs.github.io/phytest/.