{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T17:14:17Z","timestamp":1776273257769,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Ever larger phylogenies are being constructed due to the explosion of genetic data and development of high-performance phylogenetic reconstruction algorithms. However, most methods for calculating divergence times are limited to datasets that are orders of magnitude smaller than recently published large phylogenies. Here, we present an algorithm and implementation of a divergence time method using penalized likelihood that can handle datasets of thousands of taxa. We implement a method that combines the standard derivative-based optimization with a stochastic simulated annealing approach to overcome optimization challenges. We compare this approach with existing software including r8s, PATHd8 and BEAST.<\/jats:p><jats:p>Availability: Source code, example files, binaries and documentation for treePL are available at https:\/\/github.com\/blackrim\/treePL.<\/jats:p><jats:p>Contact: \u00a0eebsmith@umich.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts492","type":"journal-article","created":{"date-parts":[[2012,8,21]],"date-time":"2012-08-21T01:12:25Z","timestamp":1345511545000},"page":"2689-2690","source":"Crossref","is-referenced-by-count":776,"title":["treePL: divergence time estimation using penalized likelihood for large phylogenies"],"prefix":"10.1093","volume":"28","author":[{"given":"Stephen A.","family":"Smith","sequence":"first","affiliation":[{"name":"1 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109 and 2Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996 USA"}]},{"given":"Brian C.","family":"O\u2019Meara","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109 and 2Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996 USA"}]}],"member":"286","published-online":{"date-parts":[[2012,8,20]]},"reference":[{"key":"2023012513141128100_bts492-B1","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1080\/10635150701613783","article-title":"Estimating divergence times in large phylogenetic trees","volume":"56","author":"Britton","year":"2007","journal-title":"Syst. Biol."},{"key":"2023012513141128100_bts492-B2","doi-asserted-by":"crossref","DOI":"10.56021\/9780801844454","volume-title":"Likelihood","author":"Edwards","year":"1992","edition":"2nd"},{"key":"2023012513141128100_bts492-B3"},{"key":"2023012513141128100_bts492-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1096-0031.2009.00255.x","article-title":"Phylogenetic analysis of 73060 taxa corroborates major eukaryotic groups","volume":"25","author":"Goloboff","year":"2009","journal-title":"Cladistics"},{"key":"2023012513141128100_bts492-B5","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1145\/229473.229474","article-title":"Algorithm 755: ADOL-C: a package for the automatic differentiation of algorithms written in C\/C++","volume":"22","author":"Griewank","year":"1996","journal-title":"ACM Trans. Math. Software"},{"key":"2023012513141128100_bts492-B6","first-page":"1137","article-title":"A study of cross-validation and bootstrap for accuracy estimation and model selection","volume-title":"Proceedings of the 14th International Joint Conference on A.I.","author":"Kohavi","year":"1995"},{"key":"2023012513141128100_bts492-B7","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1093\/oxfordjournals.molbev.a003974","article-title":"Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach","volume":"19","author":"Sanderson","year":"2002","journal-title":"Mol. Biol. Evol."},{"key":"2023012513141128100_bts492-B8","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/1471-2148-9-37","article-title":"Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches","volume":"9","author":"Smith","year":"2009","journal-title":"BMC Evol. Biol."},{"key":"2023012513141128100_bts492-B9","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1007\/0-387-27733-1_8","article-title":"Estimation of divergence times from molecular sequence data","volume-title":"Statistical Methods in Molecular Evolution","author":"Thorne","year":"2005"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/20\/2689\/48875335\/bioinformatics_28_20_2689.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/20\/2689\/48875335\/bioinformatics_28_20_2689.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,25]],"date-time":"2023-06-25T10:52:11Z","timestamp":1687690331000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/20\/2689\/203074"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,8,20]]},"references-count":9,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2012,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts492","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,10,15]]},"published":{"date-parts":[[2012,8,20]]}}}