{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T13:13:34Z","timestamp":1776258814135,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"22-23","license":[{"start":{"date-parts":[[2020,12,16]],"date-time":"2020-12-16T00:00:00Z","timestamp":1608076800000},"content-version":"vor","delay-in-days":15,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1564611"],"award-info":[{"award-number":["DBI-1564611"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genome sequencing projects have revealed frequent gains and losses of genes between species. Previous versions of our software, Computational Analysis of gene Family Evolution (CAFE), have allowed researchers to estimate parameters of gene gain and loss across a phylogenetic tree. However, the underlying model assumed that all gene families had the same rate of evolution, despite evidence suggesting a large amount of variation in rates among families.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions. These include improved support for multithreading, the explicit modeling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CAFE 5 source code, documentation, test data and a detailed manual with examples are freely available at https:\/\/github.com\/hahnlab\/CAFE5\/releases.<\/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\/btaa1022","type":"journal-article","created":{"date-parts":[[2020,11,30]],"date-time":"2020-11-30T20:30:03Z","timestamp":1606768203000},"page":"5516-5518","source":"Crossref","is-referenced-by-count":685,"title":["CAFE 5 models variation in evolutionary rates among gene families"],"prefix":"10.1093","volume":"36","author":[{"given":"F\u00e1bio K","family":"Mendes","sequence":"first","affiliation":[{"name":"Department of Biology, Indiana University , Bloomington, IN 47405, USA"},{"name":"Department of Computer Science, The University of Auckland , 1010 Auckland, New Zealand"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6856-5636","authenticated-orcid":false,"given":"Dan","family":"Vanderpool","sequence":"additional","affiliation":[{"name":"Department of Biology, Indiana University , Bloomington, IN 47405, USA"}]},{"given":"Ben","family":"Fulton","sequence":"additional","affiliation":[{"name":"Department of Biology, Indiana University , Bloomington, IN 47405, USA"},{"name":"Department of Computer Science, University Information Technology Services, Indiana University , Bloomington, IN 47405, USA"}]},{"given":"Matthew W","family":"Hahn","sequence":"additional","affiliation":[{"name":"Department of Biology, Indiana University , Bloomington, IN 47405, USA"},{"name":"Department of Computer Science, Indiana University , Bloomington, IN 47405, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,12,16]]},"reference":[{"key":"2023062803480546800_btaa1022-B1","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1093\/bioinformatics\/btr592","article-title":"Determining the evolutionary history of gene families","volume":"28","author":"Ames","year":"2012","journal-title":"Bioinformatics"},{"key":"2023062803480546800_btaa1022-B2","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1002\/ajb2.1211","article-title":"The nonrandom evolution of gene families","volume":"106","author":"Casola","year":"2019","journal-title":"Am. 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