{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T04:07:16Z","timestamp":1776312436285,"version":"3.50.1"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2021,2,9]],"date-time":"2021-02-09T00:00:00Z","timestamp":1612828800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"name":"James H. 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However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene\u2013gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining and deriving biological meaning from increasingly large phylogenomic datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PhyKIT is freely available on GitHub (https:\/\/github.com\/JLSteenwyk\/PhyKIT), PyPi (https:\/\/pypi.org\/project\/phykit\/) and the Anaconda Cloud (https:\/\/anaconda.org\/JLSteenwyk\/phykit) under the MIT license with extensive documentation and user tutorials (https:\/\/jlsteenwyk.com\/PhyKIT).<\/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\/btab096","type":"journal-article","created":{"date-parts":[[2021,2,5]],"date-time":"2021-02-05T15:31:12Z","timestamp":1612539072000},"page":"2325-2331","source":"Crossref","is-referenced-by-count":195,"title":["PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8436-595X","authenticated-orcid":false,"given":"Jacob L","family":"Steenwyk","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9367-6189","authenticated-orcid":false,"suffix":"III","given":"Thomas J","family":"Buida","sequence":"additional","affiliation":[{"name":"9 City Place #312, Nashville , TN 37209, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0068-6703","authenticated-orcid":false,"given":"Abigail L","family":"Labella","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2206-5804","authenticated-orcid":false,"given":"Yuanning","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5765-1419","authenticated-orcid":false,"given":"Xing-Xing","family":"Shen","sequence":"additional","affiliation":[{"name":"Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7248-6551","authenticated-orcid":false,"given":"Antonis","family":"Rokas","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,2,9]]},"reference":[{"key":"2023051609140687300_btab096-B1","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13104-016-2340-8","article-title":"treeman: an R package for efficient and intuitive manipulation of phylogenetic trees","volume":"10","author":"Bennett","year":"2017","journal-title":"BMC Res. 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