{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T21:29:41Z","timestamp":1775078981075,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Datamonkey is a popular web-based suite of phylogenetic analysis tools for use in evolutionary biology. Since the original release in 2005, we have expanded the analysis options to include recently developed algorithmic methods for recombination detection, evolutionary fingerprinting of genes, codon model selection, co-evolution between sites, identification of sites, which rapidly escape host-immune pressure and HIV-1 subtype assignment. The traditional selection tools have also been augmented to include recent developments in the field. Here, we summarize the analyses options currently available on Datamonkey, and provide guidelines for their use in evolutionary biology.<\/jats:p>\n               <jats:p>Availability and documentation: \u00a0http:\/\/www.datamonkey.org<\/jats:p>\n               <jats:p>Contact: \u00a0spond@ucsd.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq429","type":"journal-article","created":{"date-parts":[[2010,7,30]],"date-time":"2010-07-30T02:42:33Z","timestamp":1280457753000},"page":"2455-2457","source":"Crossref","is-referenced-by-count":1078,"title":["Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology"],"prefix":"10.1093","volume":"26","author":[{"given":"Wayne","family":"Delport","sequence":"first","affiliation":[{"name":"1 Department of Pathology, Antiviral Research Center, University of California, San Diego, CA, USA, 2British Columbia Centre for Excellence in HIV\/AIDS, Vancouver, British Columbia, Canada, 3Department of Veterinary Medicine, University of Cambridge, Cambridge, UK and 4Department of Medicine, Antiviral Research Center, University of California, San Diego, CA, USA"}]},{"given":"Art F. Y.","family":"Poon","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, Antiviral Research Center, University of California, San Diego, CA, USA, 2British Columbia Centre for Excellence in HIV\/AIDS, Vancouver, British Columbia, Canada, 3Department of Veterinary Medicine, University of Cambridge, Cambridge, UK and 4Department of Medicine, Antiviral Research Center, University of California, San Diego, CA, USA"}]},{"given":"Simon D. W.","family":"Frost","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, Antiviral Research Center, University of California, San Diego, CA, USA, 2British Columbia Centre for Excellence in HIV\/AIDS, Vancouver, British Columbia, Canada, 3Department of Veterinary Medicine, University of Cambridge, Cambridge, UK and 4Department of Medicine, Antiviral Research Center, University of California, San Diego, CA, USA"}]},{"given":"Sergei L.","family":"Kosakovsky Pond","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, Antiviral Research Center, University of California, San Diego, CA, USA, 2British Columbia Centre for Excellence in HIV\/AIDS, Vancouver, British Columbia, Canada, 3Department of Veterinary Medicine, University of Cambridge, Cambridge, UK and 4Department of Medicine, Antiviral Research Center, University of California, San Diego, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,7,29]]},"reference":[{"key":"2023012508165850800_B1","doi-asserted-by":"crossref","first-page":"2104","DOI":"10.1093\/bioinformatics\/bti263","article-title":"ProtTest: selection of best-fit models of protein evolution","volume":"21","author":"Abascal","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508165850800_B2","doi-asserted-by":"crossref","first-page":"e1000242","DOI":"10.1371\/journal.ppat.1000242","article-title":"Frequent toggling between alternative amino acids is driven by selection in HIV-1","volume":"4","author":"Delport","year":"2008","journal-title":"PLoS Pathog."},{"key":"2023012508165850800_B3","doi-asserted-by":"crossref","first-page":"e1000885","DOI":"10.1371\/journal.pcbi.1000885","article-title":"CodonTest: modeling amino-acid substitution preferences in coding sequences","volume":"6","author":"Delport","year":"2010","journal-title":"PLoS Compt. Biol."},{"key":"2023012508165850800_B4","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1007\/BF02101694","article-title":"Dating of the human-ape splitting by a molecular clock of mitochondrial DNA","volume":"21","author":"Hasegawa","year":"1985","journal-title":"Mol. Biol. Evol."},{"key":"2023012508165850800_B5","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1093\/bioinformatics\/bti320","article-title":"Datamonkey: rapid detection of selective pressure on individual sites of codon alignments","volume":"21","author":"Kosakovsky Pond","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508165850800_B6","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1093\/molbev\/msi031","article-title":"A genetic algorithm approach to detecting lineage-specific variation in selection pressure","volume":"22","author":"Kosakovsky Pond","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"2023012508165850800_B7","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1093\/molbev\/msi105","article-title":"Not so different after all: a comparison of methods for detecting amino acid sites under selection","volume":"22","author":"Kosakovsky Pond","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"2023012508165850800_B8","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bioinformatics\/bti079","article-title":"HyPhy: hypothesis testing using phylogenies","volume":"21","author":"Kosakovsky Pond","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508165850800_B9","doi-asserted-by":"crossref","first-page":"e62","DOI":"10.1371\/journal.pcbi.0020062","article-title":"Adaptation to different human populations by HIV-1 revealed by codon-based analyses","volume":"2","author":"Kosakovsky Pond","year":"2006","journal-title":"PLoS Comp. Biol."},{"key":"2023012508165850800_B10","doi-asserted-by":"crossref","first-page":"1891","DOI":"10.1093\/molbev\/msl051","article-title":"Automated phylogenetic detection of recombination using a genetic algorithm","volume":"23","author":"Kosakovsky Pond","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"2023012508165850800_B11","doi-asserted-by":"crossref","first-page":"3096","DOI":"10.1093\/bioinformatics\/btl474","article-title":"GARD: a genetic algorithm for recombination detection","volume":"22","author":"Kosakovsky Pond","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012508165850800_B12","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1093\/molbev\/msn123","article-title":"A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza a virus","volume":"25","author":"Kosakovsky Pond","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"2023012508165850800_B13","doi-asserted-by":"crossref","first-page":"e1000581","DOI":"10.1371\/journal.pcbi.1000581","article-title":"An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1","volume":"5","author":"Kosakovsky Pond","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012508165850800_B14","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1093\/molbev\/msp260","article-title":"Evolutionary fingerprinting of genes","volume":"27","author":"Kosakovsky Pond","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"2023012508165850800_B15","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":"2023012508165850800_B16","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1093\/genetics\/148.3.929","article-title":"Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene","volume":"148","author":"Nielsen","year":"1998","journal-title":"Genetics"},{"key":"2023012508165850800_B17","doi-asserted-by":"crossref","first-page":"1949","DOI":"10.1093\/bioinformatics\/btn313","article-title":"Spidermonkey: rapid detection of co-evolving sites using bayesian graphical models","volume":"24","author":"Poon","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012508165850800_B18","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1093\/oxfordjournals.molbev.a026369","article-title":"A fast algorithm for joint reconstruction of ancestral amino acid sequences","volume":"17","author":"Pupko","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"2023012508165850800_B19","doi-asserted-by":"crossref","first-page":"2493","DOI":"10.1093\/bioinformatics\/btl427","article-title":"Robust inference of positive selection from recombining coding sequences","volume":"22","author":"Scheffler","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012508165850800_B20","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/genetics\/141.4.1641","article-title":"A new method of inference of ancestral nucleotide and amino acid sequences","volume":"141","author":"Yang","year":"1995","journal-title":"Genetics"},{"key":"2023012508165850800_B21","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1093\/molbev\/msi097","article-title":"Bayes Empirical Bayes inference of amino acid sites under positive selection","volume":"22","author":"Yang","year":"2005","journal-title":"Mol. Biol. Evol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/19\/2455\/48854971\/bioinformatics_26_19_2455.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/19\/2455\/48854971\/bioinformatics_26_19_2455.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:17:32Z","timestamp":1674634652000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/19\/2455\/228720"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,7,29]]},"references-count":21,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2010,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq429","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,10,1]]},"published":{"date-parts":[[2010,7,29]]}}}