Phytest: quality control for phylogenetic analyses.
Bioinformatics
; 38(22): 5124-5125, 2022 Nov 15.
Article
in English
| MEDLINE | ID: covidwho-2062861
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/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.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
SARS-CoV-2
/
COVID-19
Type of study:
Randomized controlled trials
Limits:
Humans
Language:
English
Journal:
Bioinformatics
Journal subject:
Medical Informatics
Year:
2022
Document Type:
Article
Affiliation country:
Bioinformatics
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