{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T02:43:40Z","timestamp":1775011420435,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,7,11]],"date-time":"2019-07-11T00:00:00Z","timestamp":1562803200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Royal Commission for the Exhibition of 1851 fellowship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The fossil record is incomplete, so molecular divergence time analysis is a crucial tool in estimating evolutionary timescales. MCMCtree contained in the PAML software provides Bayesian methods to estimate divergence times of genomic-sized sequences. Here, I present MCMCtreeR, a flexible R package to prepare time priors for MCMCtree analysis and plot time-scaled phylogenies. The package provides functions to refine parameters and visualize time-calibrated node prior distributions so that these priors accurately reflect confidence in known, usually fossil, time information. After the parameters have been chosen, the package produces output files ready for MCMCtree analysis. Following analysis, the package has tools to compare prior and posterior calibrated node age distributions and produce plots of the time-scaled phylogenies. The plotting functions allow for the inclusion of age uncertainty on time-scaled phylogenies, including the display of full posterior distributions on nodes. Options also allow for the inclusion of the geological timescale, and these plotting functions are applicable with posterior age estimates from any Bayesian divergence time estimation software.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MCMCtreeR is an R package available on CRAN (https:\/\/CRAN.R-project.org\/package=MCMCtreeR). MCMCtreeR depends on the R packages ape, sn and stats4.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz554","type":"journal-article","created":{"date-parts":[[2019,7,9]],"date-time":"2019-07-09T11:11:18Z","timestamp":1562670678000},"page":"5321-5322","source":"Crossref","is-referenced-by-count":230,"title":["MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1011-3442","authenticated-orcid":false,"given":"Mark N","family":"Puttick","sequence":"first","affiliation":[{"name":"Milner Centre for Evolution, Department of Biology and Biochemistry , University of Bath, Bath, UK"}]}],"member":"286","published-online":{"date-parts":[[2019,7,11]]},"reference":[{"key":"2023013108411946300_btz554-B1","doi-asserted-by":"crossref","first-page":"e1003537","DOI":"10.1371\/journal.pcbi.1003537","article-title":"BEAST 2: a software platform for Bayesian evolutionary analysis","volume":"10","author":"Bouckaert","year":"2014","journal-title":"PLoS Comput. Biol"},{"key":"2023013108411946300_btz554-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/nrg.2015.8","article-title":"Bayesian molecular clock dating of species divergences in the genomics era","volume":"17","author":"dos Reis","year":"2016","journal-title":"Nat. Rev. Genet"},{"key":"2023013108411946300_btz554-B3","doi-asserted-by":"crossref","first-page":"2161","DOI":"10.1093\/molbev\/msr045","article-title":"Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times","volume":"28","author":"dos Reis","year":"2011","journal-title":"Mol. Biol. Evol"},{"key":"2023013108411946300_btz554-B4","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1093\/sysbio\/syw021","article-title":"RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language","volume":"65","author":"Hohna","year":"2016","journal-title":"Syst. Biol"},{"key":"2023013108411946300_btz554-B5","doi-asserted-by":"crossref","first-page":"E2274","DOI":"10.1073\/pnas.1719588115","article-title":"The timescale of early land plant evolution","volume":"115","author":"Morris","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023013108411946300_btz554-B6","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2019","journal-title":"Bioinformatics"},{"key":"2023013108411946300_btz554-B120","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1007\/BF02338839","article-title":"Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference","volume":"43","author":"Rannala","year":"1996","journal-title":"J. Mol. Evol"},{"key":"2023013108411946300_btz554-B7","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"Mrbayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space","volume":"61","author":"Ronquist","year":"2012","journal-title":"Syst. Biol"},{"key":"2023013108411946300_btz554-B8","first-page":"20170227.","article-title":"Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution","volume":"284","author":"Warnock","year":"2017","journal-title":"Proc. Biol. Sci"},{"key":"2023013108411946300_btz554-B9","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol. Biol. Evol"},{"key":"2023013108411946300_btz554-B10","doi-asserted-by":"crossref","first-page":"20150126.","DOI":"10.1098\/rstb.2015.0126","article-title":"Dating species divergences using rocks and clocks","volume":"371","author":"Yang","year":"2016","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz554\/29097653\/btz554.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/24\/5321\/48978166\/bioinformatics_35_24_5321.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/24\/5321\/48978166\/bioinformatics_35_24_5321.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:10:21Z","timestamp":1675188621000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/24\/5321\/5530964"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,7,11]]},"references-count":11,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2019,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz554","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,12,15]]},"published":{"date-parts":[[2019,7,11]]}}}