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Updated: Aug 26, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Phytest: quality control for phylogenetic analyses
Wytamma Wirth1, Simon Mutch2, Robert Turnbull2
1Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3010, Australia.
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/phytest) and can be installed via PyPI with the command 'pip install phytest'. Extensive documentation can be found at https://phytest-devs.github.io/phytest/.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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