{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T16:14:27Z","timestamp":1772813667762,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2018,5,16]],"date-time":"2018-05-16T00:00:00Z","timestamp":1526428800000},"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\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R35GM118038"],"award-info":[{"award-number":["R35GM118038"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ConSpeciFix\u2019s webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https:\/\/github.com\/Bobay-Ochman\/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty400","type":"journal-article","created":{"date-parts":[[2018,5,10]],"date-time":"2018-05-10T08:44:32Z","timestamp":1525941872000},"page":"3738-3740","source":"Crossref","is-referenced-by-count":27,"title":["<i>ConSpeciFix<\/i>: classifying prokaryotic species based on gene flow"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0438-545X","authenticated-orcid":false,"given":"Louis-Marie","family":"Bobay","sequence":"first","affiliation":[{"name":"Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, USA"}]},{"given":"Brian Shin-Hua","family":"Ellis","sequence":"additional","affiliation":[{"name":"Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA"}]},{"given":"Howard","family":"Ochman","sequence":"additional","affiliation":[{"name":"Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,5,16]]},"reference":[{"key":"2023012712365541700_bty400-B1","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1093\/gbe\/evx026","article-title":"Biological species are universal across Life's domains","volume":"9","author":"Bobay","year":"2017","journal-title":"Genome Biol. 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