{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T12:31:47Z","timestamp":1770813107065,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The comparative analysis of gene gain and loss rates is critical for understanding the role of natural selection and adaptation in shaping gene family sizes. Studying complete genome data from closely related species allows accurate estimation of gene family turnover rates. Current methods and software tools, however, are not well designed for dealing with certain kinds of functional elements, such as microRNAs or transcription factor binding sites.<\/jats:p>\n               <jats:p>Results: Here, we describe BadiRate, a new software tool to estimate family turnover rates, as well as the number of elements in internal phylogenetic nodes, by likelihood-based methods and parsimony. It implements two stochastic population models, which provide the appropriate statistical framework for testing hypothesis, such as lineage-specific gene family expansions or contractions. We have assessed the accuracy of BadiRate by computer simulations, and have also illustrated its functionality by analyzing a representative empirical dataset.<\/jats:p>\n               <jats:p>Availability: BadiRate software and documentation is available from http:\/\/www.ub.edu\/softevol\/badirate.<\/jats:p>\n               <jats:p>Contact: \u00a0jrozas@ub.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr623","type":"journal-article","created":{"date-parts":[[2011,11,12]],"date-time":"2011-11-12T02:02:15Z","timestamp":1321063335000},"page":"279-281","source":"Crossref","is-referenced-by-count":116,"title":["BadiRate: estimating family turnover rates by likelihood-based methods"],"prefix":"10.1093","volume":"28","author":[{"given":"P.","family":"Librado","sequence":"first","affiliation":[{"name":"Departament de Gen\u00e8tica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain"}]},{"given":"F. G.","family":"Vieira","sequence":"additional","affiliation":[{"name":"Departament de Gen\u00e8tica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain"}]},{"given":"J.","family":"Rozas","sequence":"additional","affiliation":[{"name":"Departament de Gen\u00e8tica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain"}]}],"member":"286","published-online":{"date-parts":[[2011,11,10]]},"reference":[{"key":"2023012511493125500_B1","doi-asserted-by":"crossref","first-page":"2914","DOI":"10.1093\/bioinformatics\/btq549","article-title":"GLOOME: gain loss mapping engine","volume":"26","author":"Cohen","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012511493125500_B2","doi-asserted-by":"crossref","first-page":"1910","DOI":"10.1093\/bioinformatics\/btq315","article-title":"Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood","volume":"26","author":"Csuros","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012511493125500_B3","doi-asserted-by":"crossref","first-page":"2087","DOI":"10.1093\/molbev\/msp123","article-title":"Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model","volume":"26","author":"Csuros","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"2023012511493125500_B4","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1093\/bioinformatics\/btl097","article-title":"CAFE: a computational tool for the study of gene family evolution","volume":"22","author":"De Bie","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012511493125500_B5","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1101\/gr.3567505","article-title":"Estimating the tempo and mode of gene family evolution from comparative genomic data","volume":"15","author":"Hahn","year":"2005","journal-title":"Genome Res."},{"key":"2023012511493125500_B6","doi-asserted-by":"crossref","first-page":"e197","DOI":"10.1371\/journal.pgen.0030197","article-title":"Gene family evolution across 12 Drosophila genomes","volume":"3","author":"Hahn","year":"2007","journal-title":"PLoS Genet."},{"key":"2023012511493125500_B7","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.tree.2003.10.013","article-title":"Model selection in ecology and evolution","volume":"19","author":"Johnson","year":"2004","journal-title":"Trends Ecol. Evol."},{"key":"2023012511493125500_B8","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1186\/1471-2105-12-426","article-title":"A Bayesian model for gene family evolution","volume":"12","author":"Liu","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012511493125500_B9","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1146\/annurev.genet.39.073003.112240","article-title":"Concerted and birth-and-death evolution of multigene families","volume":"39","author":"Nei","year":"2005","journal-title":"Annu. Rev. Genet."},{"key":"2023012511493125500_B10","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1093\/gbe\/evq009","article-title":"Origins and evolution of microRNA genes in Drosophila species","volume":"2","author":"Nozawa","year":"2010","journal-title":"Genome Biol. Evol."},{"key":"2023012511493125500_B11","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-86659-3","volume-title":"Evolution by Gene Duplication.","author":"Ohno","year":"1970"},{"key":"2023012511493125500_B12","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1038\/hdy.2009.55","article-title":"Molecular evolution of the major chemosensory gene families in insects","volume":"103","author":"Sanchez-Gracia","year":"2009","journal-title":"Heredity"},{"key":"2023012511493125500_B13","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1093\/gbe\/evr033","article-title":"Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: origin and evolutionary history of the chemosensory system","volume":"3","author":"Vieira","year":"2010","journal-title":"Genome Biol. 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