Phytest: quality control for phylogenetic analyses

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.

Automated summary

As genetic sequencing and real-time pipelines become more prevalent, the ability to automatically conduct quality control checks on phylogenetic analyses is becoming increasingly important. Phytest is a tool that automates quality control checks on sequences, trees, and metadata during phylogenetic analyses and easily integrates into existing pipelines.