{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T05:32:45Z","timestamp":1784093565425,"version":"3.55.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2017,2,8]],"date-time":"2017-02-08T00:00:00Z","timestamp":1486512000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"NSF AVATOL","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF DEB","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx: a collection of programs written in C\u2009++\u2009to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix\/GNU\/Linux command line tools, individual programs perform a single task and operate on standard I\/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation and example files are freely available under the GNU General Public License at https:\/\/github.com\/FePhyFoFum\/phyx<\/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\/btx063","type":"journal-article","created":{"date-parts":[[2017,2,8]],"date-time":"2017-02-08T06:31:41Z","timestamp":1486535501000},"page":"1886-1888","source":"Crossref","is-referenced-by-count":313,"title":["Phyx: phylogenetic tools for unix"],"prefix":"10.1093","volume":"33","author":[{"given":"Joseph W","family":"Brown","sequence":"first","affiliation":[{"name":"Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph F","family":"Walker","sequence":"additional","affiliation":[{"name":"Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen A","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,2,8]]},"reference":[{"key":"2023020205480321100_btx063-B1","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1093\/oxfordjournals.molbev.a004175","article-title":"Bayesian model adequacy and choice in phylogenetics","volume":"19","author":"Bollback","year":"2002","journal-title":"Mol. 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