{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T22:42:31Z","timestamp":1775601751800,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1019,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In recent years, there has been an increasing interest in the potential of codon substitution models for a variety of applications. However, the computational demands of these models have sometimes lead to the adoption of oversimplified assumptions, questionable statistical methods or a limited focus on small data sets.<\/jats:p>\n               <jats:p>Results: Here, we offer a scalable, message-passing-interface-based Bayesian implementation of site-heterogeneous codon models in the mutation-selection framework. Our software jointly infers the global mutational parameters at the nucleotide level, the branch lengths of the tree and a Dirichlet process governing across-site variation at the amino acid level. We focus on an example estimation of the distribution of selection coefficients from an alignment of several hundred sequences of the influenza PB2 gene, and highlight the site-specific characterization enabled by such a modeling approach. Finally, we discuss future potential applications of the software for conducting evolutionary inferences.<\/jats:p>\n               <jats:p>Availability and implementation: The models are implemented within the PhyloBayes-MPI package, (available at phylobayes.org) along with usage details in the accompanying manual.<\/jats:p>\n               <jats:p>Contact: \u00a0nicolas.rodrigue@ucalgary.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt729","type":"journal-article","created":{"date-parts":[[2013,12,19]],"date-time":"2013-12-19T06:21:56Z","timestamp":1387434116000},"page":"1020-1021","source":"Crossref","is-referenced-by-count":75,"title":["Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package"],"prefix":"10.1093","volume":"30","author":[{"given":"Nicolas","family":"Rodrigue","sequence":"first","affiliation":[{"name":"1 Department of Mathematics and Statistics, University of Calgary, 2500 University Drive NW, Calgary AB T2N 1N4, Canada and 2UMR CNRS 5558 - LBBE, Universit\u00e9 Lyon 1, Villeurbanne Cedex, France"}]},{"given":"Nicolas","family":"Lartillot","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics and Statistics, University of Calgary, 2500 University Drive NW, Calgary AB T2N 1N4, Canada and 2UMR CNRS 5558 - LBBE, Universit\u00e9 Lyon 1, Villeurbanne Cedex, France"}]}],"member":"286","published-online":{"date-parts":[[2013,12,18]]},"reference":[{"key":"2023012710451726800_btt729-B1","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1093\/acprof:osobl\/9780199601165.003.0011","article-title":"The future of codon models in studies of molecular function: ancestral reconstruction and clade models of functional divergence","volume-title":"Codon Evolution","author":"Chang","year":"2012"},{"key":"2023012710451726800_btt729-B2","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/molbev\/msp228","article-title":"Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories","volume":"27","author":"de Koning","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"2023012710451726800_btt729-B3","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1093\/molbev\/mst034","article-title":"CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models","volume":"30","author":"Gil","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"2023012710451726800_btt729-B4","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1093\/oxfordjournals.molbev.a025995","article-title":"Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies","volume":"15","author":"Halpern","year":"1998","journal-title":"Mol. Biol. Evol."},{"key":"2023012710451726800_btt729-B5","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1093\/sysbio\/syt022","article-title":"PhyloBayes-MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment","volume":"62","author":"Lartillot","year":"2013","journal-title":"Syst. Biol."},{"key":"2023012710451726800_btt729-B6","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1093\/molbev\/mss217","article-title":"Integrating sequence variation and protein structure to identify sites under selection","volume":"30","author":"Meyer","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"2023012710451726800_btt729-B7","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1534\/genetics.112.145722","article-title":"On the statistical interpretation of site-specific variables in phylogeny-based substitution models","volume":"193","author":"Rodrigue","year":"2013","journal-title":"Genetics"},{"key":"2023012710451726800_btt729-B8","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":"2023012710451726800_btt729-B9","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1534\/genetics.111.136432","article-title":"Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models","volume":"190","author":"Tamuri","year":"2012","journal-title":"Genetics"},{"key":"2023012710451726800_btt729-B10","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/acprof:osobl\/9780199601165.003.0007","article-title":"Codon models as a vehicle for reconciling population genetics with inter-specific sequence data","volume-title":"Codon Evolution","author":"Thorne","year":"2012"},{"key":"2023012710451726800_btt729-B11","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1093\/molbev\/msm284","article-title":"Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage","volume":"25","author":"Yang","year":"2008","journal-title":"Mol. Biol. Evol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/7\/1020\/48922117\/bioinformatics_30_7_1020.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/7\/1020\/48922117\/bioinformatics_30_7_1020.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:14:41Z","timestamp":1674818081000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/7\/1020\/234902"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,12,18]]},"references-count":11,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2014,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt729","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,4,1]]},"published":{"date-parts":[[2013,12,18]]}}}