{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T01:06:50Z","timestamp":1773277610247,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Mapping character state changes over phylogenetic trees is central to the study of evolution. However, current probabilistic methods for generating such mappings are ill-suited to certain types of evolutionary models, in particular, the widely used models of codon substitution.<\/jats:p>\n               <jats:p>Results: We describe a general method, based on a uniformization technique, which can be utilized to generate realizations of a Markovian substitution process conditional on an alignment of character states and a given tree topology. The method is applicable under a wide range of evolutionary models, and to illustrate its usefulness in practice, we embed it within a data augmentation-based Markov chain Monte Carlo sampler, for approximating posterior distributions under previously proposed codon substitution models. The sampler is found to be more efficient than the conventional pruning-based sampler with the decorrelation times between draws from the posterior reduced by a factor of 20 or more.<\/jats:p>\n               <jats:p>Contact: \u00a0nicolas.rodrigue@umontreal.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm532","type":"journal-article","created":{"date-parts":[[2007,11,15]],"date-time":"2007-11-15T01:25:39Z","timestamp":1195089939000},"page":"56-62","source":"Crossref","is-referenced-by-count":41,"title":["Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models"],"prefix":"10.1093","volume":"24","author":[{"given":"Nicolas","family":"Rodrigue","sequence":"first","affiliation":[{"name":"1 Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, C.P. 6821, Succ. Centre-ville, Montr\u00e9al, Qu\u00e9bec Canada, H3C 3J7 and 2Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier, URM 5506, CNRS-Universit\u00e9 de Montpellier 2, Montpellier, France"}]},{"given":"Herv\u00e9","family":"Philippe","sequence":"additional","affiliation":[{"name":"1 Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, C.P. 6821, Succ. Centre-ville, Montr\u00e9al, Qu\u00e9bec Canada, H3C 3J7 and 2Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier, URM 5506, CNRS-Universit\u00e9 de Montpellier 2, Montpellier, France"}]},{"given":"Nicolas","family":"Lartillot","sequence":"additional","affiliation":[{"name":"1 Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, C.P. 6821, Succ. Centre-ville, Montr\u00e9al, Qu\u00e9bec Canada, H3C 3J7 and 2Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier, URM 5506, CNRS-Universit\u00e9 de Montpellier 2, Montpellier, France"}]}],"member":"286","published-online":{"date-parts":[[2007,11,14]]},"reference":[{"key":"2023020209443478100_B1","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/1471-2105-7-88","article-title":"Simmap: stochastic character mapping of discrete traits on phylogenies","volume":"7","author":"Bollback","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023020209443478100_B2","doi-asserted-by":"crossref","first-page":"S126","DOI":"10.1093\/bioinformatics\/bti1032","article-title":"Detecting coevolving amino acid sites using Bayesian mutational mapping","volume":"21","author":"Dimmic","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020209443478100_B3","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1093\/molbev\/msl175","article-title":"A combined empirical and mechanistic codon model","volume":"24","author":"Doron-Faigenboim","year":"2006","journal-title":"Mol. Biol. Evol"},{"key":"2023020209443478100_B4","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1111\/j.1467-9868.2006.00566.x","article-title":"An exact Gibbs sampler for the Markov-modulated Poisson process","volume":"68","author":"Fearnhead","year":"2006","journal-title":"J. R. Statist. Soc. B"},{"key":"2023020209443478100_B5","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: a maximum likelihood approach","volume":"17","author":"Felsenstein","year":"1981","journal-title":"J. Mol. Evol"},{"key":"2023020209443478100_B6","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1198\/016214504000000458","article-title":"Parameterization and Baysian modeling","volume":"99","author":"Gelman","year":"2004","journal-title":"J. Am. Stat. Assoc"},{"key":"2023020209443478100_B7","first-page":"725","article-title":"A codon-based model of nucleotide substitution for protein-coding DNA sequences","volume":"11","author":"Goldman","year":"1994","journal-title":"Mol. Biol. Evol"},{"key":"2023020209443478100_B8","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1287\/opre.32.2.343","article-title":"The randomization technique as a modeling tool and solution procedure for transient Markov processes","volume":"32","author":"Gross","year":"1984","journal-title":"Oper. Res"},{"key":"2023020209443478100_B9","doi-asserted-by":"crossref","first-page":"12957","DOI":"10.1073\/pnas.0402177101","article-title":"Modeling the site-specific variation of selection patterns along lineages","volume":"101","author":"Guindon","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020209443478100_B10","doi-asserted-by":"crossref","DOI":"10.1198\/106186008X289010","article-title":"A Markov chain Monte Carlo expectation maximization algorithm for statistical analysis of DNA sequence evolution with neighbour-dependent substitution rates","author":"Hobolth","year":"2008","journal-title":"J. Comput. Graph. Stat"},{"key":"2023020209443478100_B11","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1093\/oxfordjournals.molbev.a004128","article-title":"Testing the covariotide model of DNA substitution","volume":"19","author":"Huelsenbeck","year":"2001","journal-title":"Mol. Biol. Evol"},{"key":"2023020209443478100_B12","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1007\/s00239-004-2588-9","article-title":"Bayesian estimation of positively selected sites","volume":"58","author":"Huelsenbeck","year":"2004","journal-title":"J. Mol. Evol"},{"key":"2023020209443478100_B13","doi-asserted-by":"crossref","first-page":"6263","DOI":"10.1073\/pnas.0508279103","article-title":"A Dirichlet process model for detecting positive selection in protein-coding DNA sequences","volume":"103","author":"Huelsenbeck","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020209443478100_B14","first-page":"87","article-title":"Markoff chains as an aid in the study of Markoff processes","volume":"36","author":"Jensen","year":"1953","journal-title":"Skandinavisk Aktuarietidskriff"},{"key":"2023020209443478100_B15","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1239\/aap\/1013540176","article-title":"Probabilistic models of DNA sequence evolution with context dependent rates of substitution","volume":"32","author":"Jensen","year":"2000","journal-title":"Adv. Appl. Probab"},{"key":"2023020209443478100_B16","doi-asserted-by":"crossref","first-page":"1871","DOI":"10.1093\/molbev\/msh198","article-title":"Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference","volume":"21","author":"Krishnan","year":"2004","journal-title":"Mol. Biol. Evol"},{"key":"2023020209443478100_B17","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1089\/cmb.2006.13.1701","article-title":"Conjugate sampling for phylogenetic models","volume":"13","author":"Lartillot","year":"2006","journal-title":"J. Comput. Biol"},{"key":"2023020209443478100_B18","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1093\/molbev\/msh112","article-title":"A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process","volume":"21","author":"Lartillot","year":"2004","journal-title":"Mol. Biol. Evol"},{"key":"2023020209443478100_B19","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1080\/10635150500541599","article-title":"Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation","volume":"55","author":"Mateiu","year":"2006","journal-title":"Syst. Biol"},{"key":"2023020209443478100_B20","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1080\/10635150290102393","article-title":"Mapping mutations on phylogenies","volume":"51","author":"Nielsen","year":"2002","journal-title":"Syst. Biol"},{"key":"2023020209443478100_B21","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1080\/10635150490468675","article-title":"A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data","volume":"53","author":"Pagel","year":"2004","journal-title":"Syst. Biol"},{"key":"2023020209443478100_B22","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1093\/oxfordjournals.molbev.a003859","article-title":"A dependent rates model and MCMC based methodology for the maximum likelihood analysis of sequences with overlapping reading frames","volume":"18","author":"Pedersen","year":"2001","journal-title":"Mol. Biol. Evol"},{"key":"2023020209443478100_B23","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1080\/10635150500354688","article-title":"An empirical examination of the utility of codon substitution models in phylogeny reconstruction","volume":"54","author":"Ren","year":"2005","journal-title":"Syst. Biol"},{"key":"2023020209443478100_B24","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-4145-2","volume-title":"Monte Carlo Statistical Methods.","author":"Robert","year":"2004"},{"key":"2023020209443478100_B25","doi-asserted-by":"crossref","first-page":"1692","DOI":"10.1093\/molbev\/msg184","article-title":"Protein evolution with dependence among codons due to tertiary structure","volume":"18","author":"Robinson","year":"2003","journal-title":"Mol. Biol. Evol"},{"key":"2023020209443478100_B26","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.gene.2004.12.011","article-title":"Site interdependence attributed to tertiary structure in amino acid sequence evolution","volume":"347","author":"Rodrigue","year":"2005","journal-title":"Gene"},{"key":"2023020209443478100_B27","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.1093\/molbev\/msl041","article-title":"Assessing site-interdependent phylogenetic models of sequence evolution","volume":"23","author":"Rodrigue","year":"2006","journal-title":"Mol. Biol. Evol"},{"key":"2023020209443478100_B28","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1080\/10635150701611258","article-title":"Exploring fast computational strategies for probabilistic phylogenetic analysis","volume":"56","author":"Rodrigue","year":"2007","journal-title":"Syst. Biol"},{"key":"2023020209443478100_B29","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/S0025-5564(97)00081-3","article-title":"Modeling the covarion hypothesis of nucleotide substitution","volume":"147","author":"Tuffley","year":"1998","journal-title":"Math. Biosci"},{"key":"2023020209443478100_B30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1198\/10618600152418584","article-title":"The art of data augmentation","volume":"10","author":"van Dyk","year":"2001","journal-title":"J. Comput. Graph. Stat"},{"key":"2023020209443478100_B31","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1093\/oxfordjournals.molbev.a003981","article-title":"Codon substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes","volume":"19","author":"Yang","year":"2002","journal-title":"Mol. Biol. Evol"},{"key":"2023020209443478100_B32","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/genetics\/155.1.431","article-title":"Codon-substitution models for heterogeneous selection pressure at amino acid sites","volume":"155","author":"Yang","year":"2000","journal-title":"Genetics"},{"key":"2023020209443478100_B33","doi-asserted-by":"crossref","first-page":"1525","DOI":"10.1093\/molbev\/msl015","article-title":"Dependence among sites in RNA evolution","volume":"23","author":"Yu","year":"2006","journal-title":"Mol. Biol. Evol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/1\/56\/49043967\/bioinformatics_24_1_56.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/1\/56\/49043967\/bioinformatics_24_1_56.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T10:03:54Z","timestamp":1675332234000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/1\/56\/205240"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,11,14]]},"references-count":33,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm532","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,1,1]]},"published":{"date-parts":[[2007,11,14]]}}}