{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T06:16:38Z","timestamp":1772950598048,"version":"3.50.1"},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"suppl_1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2003,7,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Score-based progressive alignment algorithms do dynamic programming on successive branches of a guide tree. The analogous probabilistic construct is an Evolutionary HMM. This is a multiple-sequence hidden Markov model (HMM) made by combining transducers (conditionally normalised Pair HMMs) on the branches of a phylogenetic tree.<\/jats:p>\n               <jats:p>Methods: We present general algorithms for constructing an Evolutionary HMM from any Pair HMM and for doing dynamic programming to any Multiple-sequence HMM.<\/jats:p>\n               <jats:p>Results: Our prototype implementation, Handel, is based on the Thorne-Kishino-Felsenstein evolutionary model and is benchmarked using structural reference alignments.<\/jats:p>\n               <jats:p>Availability: Handel can be downloaded under GPL from www.biowiki.org\/Handel<\/jats:p>","DOI":"10.1093\/bioinformatics\/btg1019","type":"journal-article","created":{"date-parts":[[2003,7,10]],"date-time":"2003-07-10T23:49:03Z","timestamp":1057880943000},"page":"i147-i157","source":"Crossref","is-referenced-by-count":40,"title":["Using guide trees to construct multiple-sequence evolutionary HMMs"],"prefix":"10.1093","volume":"19","author":[{"given":"I.","family":"Holmes","sequence":"first","affiliation":[{"name":"Department of Statistics, University of Oxford. 1 South Parks Road, Oxford OX1 3TG, UK"}]}],"member":"286","published-online":{"date-parts":[[2003,7,3]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_1\/i147\/227868","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_1\/i147\/227868","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:46:02Z","timestamp":1674672362000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_1\/i147\/227868"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,7,3]]},"references-count":0,"journal-issue":{"issue":"suppl_1","published-print":{"date-parts":[[2003,7,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btg1019","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2003,7,3]]},"published":{"date-parts":[[2003,7,3]]}}}