{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T13:26:02Z","timestamp":1760016362319},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We describe handalign, a software package for Bayesian reconstruction of phylogenetic history. The underlying model of sequence evolution describes indels and substitutions. Alignments, trees and model parameters are all treated as jointly dependent random variables and sampled via Metropolis\u2013Hastings Markov chain Monte Carlo (MCMC), enabling systematic statistical parameter inference and hypothesis testing. handalign implements several different MCMC proposal kernels, allows sampling from arbitrary target distributions via Hastings ratios, and uses standard file formats for trees, alignments and models.<\/jats:p>\n               <jats:p>Availability and Implementation: Installation and usage instructions are at http:\/\/biowiki.org\/HandAlign<\/jats:p>\n               <jats:p>Contact: \u00a0ihh@berkeley.edu<\/jats:p>\n               <jats:p>Supplementary information:Supplementary material is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts058","type":"journal-article","created":{"date-parts":[[2012,1,29]],"date-time":"2012-01-29T01:14:57Z","timestamp":1327799697000},"page":"1170-1171","source":"Crossref","is-referenced-by-count":18,"title":["HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction"],"prefix":"10.1093","volume":"28","author":[{"given":"Oscar","family":"Westesson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lars","family":"Barquist","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,1,28]]},"reference":[{"key":"2023012711534778700_B1","article-title":"Efficient inference in phylogenetic InDel trees","volume-title":"Advances in Neural Information Processing Systems 21 (NIPS)","author":"Bouchard-C\u00f4t\u00e9","year":"2009"},{"key":"2023012711534778700_B2","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1093\/bioinformatics\/17.9.803","article-title":"Evolutionary HMMs: a Bayesian approach to multiple alignment","volume":"17","author":"Holmes","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012711534778700_B3","doi-asserted-by":"crossref","first-page":"10373","DOI":"10.1016\/S0021-9258(18)86956-3","article-title":"Assignment of intrachain disulfide bonds and characterization of potential glycosylation sites of the type 1 recombinant human immunodeficiency virus envelope glycoprotein (gp120) expressed in Chinese hamster ovary cells","volume":"265","author":"Leonard","year":"1990","journal-title":"J. of Biol. Chem."},{"key":"2023012711534778700_B4","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1093\/molbev\/msh043","article-title":"A long indel model for evolutionary sequence alignment","volume":"21","author":"Mikl\u00f3s","year":"2004","journal-title":"Mol. Biol. Evol."},{"key":"2023012711534778700_B5","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1080\/10635150590947041","article-title":"Joint Bayesian estimation of alignment and phylogeny","volume":"54","author":"Redelings","year":"2005","journal-title":"Systematic Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/8\/1170\/48930469\/bioinformatics_28_8_1170.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/8\/1170\/48930469\/bioinformatics_28_8_1170.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:14:33Z","timestamp":1674821673000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/8\/1170\/194682"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1,28]]},"references-count":5,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2012,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts058","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2012,4]]},"published":{"date-parts":[[2012,1,28]]}}}