{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,13]],"date-time":"2026-09-13T20:09:00Z","timestamp":1789330140124,"version":"build-2803163510"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Departament de Recerca i Universitats de la Generalitat de Catalunya","award":["GRC 2021 SGR 0467"],"award-info":[{"award-number":["GRC 2021 SGR 0467"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for predefined groups of species representing the phenotypic values targeted by the user.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CAAStools source code is available at http:\/\/github.com\/linudz\/caastools, along with documentation and examples.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad623","type":"journal-article","created":{"date-parts":[[2023,10,13]],"date-time":"2023-10-13T10:00:37Z","timestamp":1697191237000},"source":"Crossref","is-referenced-by-count":12,"title":["CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0844-512X","authenticated-orcid":false,"given":"Fabio","family":"Barteri","sequence":"first","affiliation":[{"name":"IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra . C. Doctor Aiguader 88 , Barcelona 08003, Spain"},{"name":"BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation , C\/ Wellington 30 , Barcelona 08006, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Valenzuela","sequence":"additional","affiliation":[{"name":"IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra . C. Doctor Aiguader 88 , Barcelona 08003, Spain"},{"name":"BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation , C\/ Wellington 30 , Barcelona 08006, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6838-9479","authenticated-orcid":false,"given":"Xavier","family":"Farr\u00e9","sequence":"additional","affiliation":[{"name":"Genomes for Life-GCAT Lab, GermanTrias i Pujol Research Institute (IGTP) , Cam\u00ed de les Escoles, s\/n , Badalona 08916, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1912-9667","authenticated-orcid":false,"given":"David","family":"de Juan","sequence":"additional","affiliation":[{"name":"IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra . C. Doctor Aiguader 88 , Barcelona 08003, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerard","family":"Muntan\u00e9","sequence":"additional","affiliation":[{"name":"IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra . C. Doctor Aiguader 88 , Barcelona 08003, Spain"},{"name":"Institut d\u2019Investigaci\u00f3 Sanit\u00e0ria Pere Virgili (IISPV), Hospital Universitari Institut Pere Mata, Universitat Rovira i Virgili . Avda. Josep Laporte, 2 \u2013 Planta 0 \u2013 E2 color taronja , Reus 43204, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red en Salud Mental (CIBERSAM) , Av. Monforte de Lemos, 3-5. Pabell\u00f3n 11. Planta 0 . Madrid 28029, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Borja","family":"Esteve-Altava","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory , Meyerhofstra\u00dfe 1 , Heidelberg 69117, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arcadi","family":"Navarro","sequence":"additional","affiliation":[{"name":"IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra . C. Doctor Aiguader 88 , Barcelona 08003, Spain"},{"name":"BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation , C\/ Wellington 30 , Barcelona 08006, Spain"},{"name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) and Universitat Pompeu Fabra , Pg. Llu\u00eds Companys 23 , Barcelona 08010, Spain"},{"name":"Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , C. Doctor Aiguader N88 , Barcelona 08003, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,10,16]]},"reference":[{"key":"2023102510310098900_btad623-B1","doi-asserted-by":"crossref","first-page":"1909","DOI":"10.1093\/molbev\/msp103","article-title":"Phylogenomics of C4 photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence","volume":"26","author":"Besnard","year":"2009","journal-title":"Mol Biol Evol"},{"key":"2023102510310098900_btad623-B2","doi-asserted-by":"crossref","first-page":"8986","DOI":"10.1073\/pnas.0900233106","article-title":"Evidence for an ancient adaptive episode of convergent molecular evolution","volume":"106","author":"Castoe","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"key":"2023102510310098900_btad623-B3","doi-asserted-by":"crossref","first-page":"2170","DOI":"10.1111\/2041-210X.13071","article-title":"Detecting the molecular basis of phenotypic convergence","volume":"9","author":"Chabrol","year":"2018","journal-title":"Methods Ecol Evol"},{"key":"2023102510310098900_btad623-B4","doi-asserted-by":"crossref","first-page":"4948","DOI":"10.1093\/molbev\/msab219","article-title":"Comparative analysis of mammal genomes unveils key genomic variability for human life span","volume":"38","author":"Farr\u00e9","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2023102510310098900_btad623-B5","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/ng.3198","article-title":"Convergent evolution of the genomes of marine mammals","volume":"47","author":"Foote","year":"2015","journal-title":"Nat Genet"},{"key":"2023102510310098900_btad623-B6","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1093\/nsr\/nwaa027","article-title":"Convergent adaptation of the genomes of woody plants at the land\u2013sea interface","volume":"7","author":"He","year":"2020","journal-title":"Natl Sci Rev"},{"key":"2023102510310098900_btad623-B7","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1093\/molbev\/msz197","article-title":"HyPhy 2.5\u2014a customizable platform for evolutionary hypothesis testing using phylogenies","volume":"37","author":"Kosakovsky Pond","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2023102510310098900_btad623-B8","doi-asserted-by":"crossref","first-page":"4815","DOI":"10.1093\/bioinformatics\/btz468","article-title":"RERconverge: an R package for associating evolutionary rates with convergent traits","volume":"35","author":"Kowalczyk","year":"2019","journal-title":"Bioinformatics"},{"key":"2023102510310098900_btad623-B9","doi-asserted-by":"crossref","first-page":"13959","DOI":"10.1073\/pnas.0802097105","article-title":"The hearing gene Prestin reunites echolocating bats","volume":"105","author":"Li","year":"2008","journal-title":"Proc Natl Acad Sci USA"},{"key":"2023102510310098900_btad623-B10","doi-asserted-by":"crossref","first-page":"1990","DOI":"10.1093\/molbev\/msy105","article-title":"Biological processes modulating longevity across primates: a phylogenetic genome-phenome analysis","volume":"35","author":"Muntan\u00e9","year":"2018","journal-title":"Mol Biol Evol"},{"key":"2023102510310098900_btad623-B11","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1038\/nature12511","article-title":"Genome-wide signatures of convergent evolution in echolocating mammals","volume":"502","author":"Parker","year":"2013","journal-title":"Nature"},{"key":"2023102510310098900_btad623-B12","doi-asserted-by":"crossref","first-page":"2296","DOI":"10.1093\/molbev\/msy114","article-title":"Accurate detection of convergent amino-acid evolution with PCOC","volume":"35","author":"Rey","year":"2018","journal-title":"Mol Biol Evol"},{"key":"2023102510310098900_btad623-B13","doi-asserted-by":"crossref","first-page":"20180234","DOI":"10.1098\/rstb.2018.0234","article-title":"Detecting adaptive convergent amino acid evolution","volume":"374","author":"Rey","year":"2019","journal-title":"Phil Trans R Soc B Biol Sci"},{"key":"2023102510310098900_btad623-B14","doi-asserted-by":"crossref","first-page":"4629","DOI":"10.1073\/pnas.0910915107","article-title":"Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles","volume":"107","author":"Rodrigue","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"2023102510310098900_btad623-B15","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1016\/j.jtbi.2016.05.029","article-title":"A comparison of ancestral state reconstruction methods for quantitative characters","volume":"404","author":"Royer-Carenzi","year":"2016","journal-title":"J Theor Biol"},{"key":"2023102510310098900_btad623-B16","doi-asserted-by":"crossref","first-page":"3004","DOI":"10.1093\/molbev\/msab068","article-title":"Phylogenetic permulations: a statistically rigorous approach to measure confidence in associations in a phylogenetic context","volume":"38","author":"Saputra","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2023102510310098900_btad623-B17","doi-asserted-by":"crossref","first-page":"925","DOI":"10.3389\/fgene.2019.00925","article-title":"Convergent evolution of mitochondrial genes in deep-sea fishes","volume":"10","author":"Shen","year":"2019","journal-title":"Front Genet"},{"key":"2023102510310098900_btad623-B0240513","doi-asserted-by":"crossref","first-page":"1232","DOI":"10.1093\/molbev\/msv013","article-title":"Determining the null model for detecting adaptive convergence from genomic data: A case study using echolocating mammals","volume":"32","author":"Thomas","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2023102510310098900_btad623-B18","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1007\/s00239-013-9557-0","article-title":"The site-wise log-likelihood score is a good predictor of genes under positive selection","volume":"76","author":"Wang","year":"2013","journal-title":"J Mol Evol"},{"key":"2023102510310098900_btad623-B19","first-page":"1008","article-title":"Genome-Wide convergence during evolution of mangroves from woody plants","volume":"34","author":"Xu","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2023102510310098900_btad623-B20","first-page":"555","article-title":"PAML: a program package for phylogenetic analysis by maximum likelihood","volume":"13","author":"Yang","year":"1997","journal-title":"Comput Appl Biosci"},{"key":"2023102510310098900_btad623-B21","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1126\/science.1251385","article-title":"Comparative genomics reveals insights into avian genome evolution and adaptation","volume":"346","author":"Zhang","year":"2014","journal-title":"Science"},{"key":"2023102510310098900_btad623-B22","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1093\/oxfordjournals.molbev.a025789","article-title":"Detection of convergent and parallel evolution at the amino acid sequence level","volume":"14","author":"Zhang","year":"1997","journal-title":"Mol Biol Evol"},{"key":"2023102510310098900_btad623-B23","doi-asserted-by":"crossref","first-page":"2085","DOI":"10.1093\/molbev\/msv091","article-title":"Are convergent and parallel amino acid substitutions in protein evolution more prevalent than neutral expectations?","volume":"32","author":"Zou","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2023102510310098900_btad623-B24","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1093\/molbev\/msv014","article-title":"No genome-wide protein sequence convergence for echolocation","volume":"32","author":"Zou","year":"2015","journal-title":"Mol Biol Evol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad623\/52188222\/btad623.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/10\/btad623\/52516198\/btad623.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/10\/btad623\/52516198\/btad623.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,25]],"date-time":"2023-10-25T06:31:21Z","timestamp":1698215481000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad623\/7319365"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,10,1]]},"references-count":25,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2023,10,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad623","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.12.14.520422","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,10,1]]},"published":{"date-parts":[[2023,10,1]]},"article-number":"btad623"}}