{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:16Z","timestamp":1772138056311,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T00:00:00Z","timestamp":1665100800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DE190100805"],"award-info":[{"award-number":["DE190100805"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Australian National Health and Medical Research Council"},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["APP1157586"],"award-info":[{"award-number":["APP1157586"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Phytest is a phylogenetic analysis testing program that easily integrates into existing phylogenetic pipelines. We demonstrate the utility of Phytest with real-world examples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Phytest source code is available on GitHub (https:\/\/github.com\/phytest-devs\/phytest) and can be installed via PyPI with the command \u2018pip install phytest\u2019. Extensive documentation can be found at https:\/\/phytest-devs.github.io\/phytest\/.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac664","type":"journal-article","created":{"date-parts":[[2022,10,4]],"date-time":"2022-10-04T08:43:08Z","timestamp":1664872988000},"page":"5124-5125","source":"Crossref","is-referenced-by-count":0,"title":["Phytest: quality control for phylogenetic analyses"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7070-0078","authenticated-orcid":false,"given":"Wytamma","family":"Wirth","sequence":"first","affiliation":[{"name":"Peter Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne 3010, Australia"}]},{"given":"Simon","family":"Mutch","sequence":"additional","affiliation":[{"name":"Melbourne Data Analytics Platform, University of Melbourne , Melbourne 3010, Australia"}]},{"given":"Robert","family":"Turnbull","sequence":"additional","affiliation":[{"name":"Melbourne Data Analytics Platform, University of Melbourne , Melbourne 3010, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2863-0907","authenticated-orcid":false,"given":"Sebastian","family":"Duchene","sequence":"additional","affiliation":[{"name":"Peter Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne 3010, Australia"}]}],"member":"286","published-online":{"date-parts":[[2022,10,7]]},"reference":[{"key":"2022112014200319700_btac664-B1","doi-asserted-by":"crossref","first-page":"e1006650","DOI":"10.1371\/journal.pcbi.1006650","article-title":"Beast 2.5: an advanced software platform for Bayesian evolutionary analysis","volume":"15","author":"Bouckaert","year":"2019","journal-title":"PLoS Comput. 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