{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,3,8]],"date-time":"2024-03-08T08:36:47Z","timestamp":1709887007867},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Full-length DNA and protein sequences that span the entire length of a gene are ideally used for multiple sequence alignments (MSAs) and the subsequent inference of their relationships. Frequently, however, MSAs contain a substantial amount of missing data. For example, expressed sequence tags (ESTs), which are partial sequences of expressed genes, are the predominant source of sequence data for many organisms. The patterns of missing data typical for EST-derived alignments greatly compromise the accuracy of estimated phylogenies.<\/jats:p>\n               <jats:p>Results: We present a statistical method for inferring phylogenetic trees from EST-based incomplete MSA data. We propose a class of hierarchical models for modeling pairwise distances between the sequences, and develop a fully Bayesian approach for estimation of the model parameters. Once the distance matrix is estimated, the phylogenetic tree may be constructed by applying neighbor-joining (or any other algorithm of choice). We also show that maximizing the marginal likelihood from the Bayesian approach yields similar results to a profile likelihood estimation. The proposed methods are illustrated using simulated protein families, for which the true phylogeny is known, and one real protein family.<\/jats:p>\n               <jats:p>Availability: R code for fitting these models are available from: http:\/\/people.bu.edu\/gupta\/software.htm.<\/jats:p>\n               <jats:p>Contact: \u00a0gupta@bu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp015","type":"journal-article","created":{"date-parts":[[2009,1,16]],"date-time":"2009-01-16T01:44:59Z","timestamp":1232070299000},"page":"592-598","source":"Crossref","is-referenced-by-count":4,"title":["A hierarchical model for incomplete alignments in phylogenetic inference"],"prefix":"10.1093","volume":"25","author":[{"given":"Fuxia","family":"Cheng","sequence":"first","affiliation":[{"name":"1 Department of Mathematics, Illinois State University, Normal, IL, USA, 2Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany, 3Department of Biostatistics, Boston University, Boston, MA, 4Department of Biostatistics and 5Department of Biology, University of North Carolina at Chapel Hill, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefanie","family":"Hartmann","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics, Illinois State University, Normal, IL, USA, 2Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany, 3Department of Biostatistics, Boston University, Boston, MA, 4Department of Biostatistics and 5Department of Biology, University of North Carolina at Chapel Hill, USA"},{"name":"1 Department of Mathematics, Illinois State University, Normal, IL, USA, 2Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany, 3Department of Biostatistics, Boston University, Boston, MA, 4Department of Biostatistics and 5Department of Biology, University of North Carolina at Chapel Hill, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mayetri","family":"Gupta","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics, Illinois State University, Normal, IL, USA, 2Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany, 3Department of Biostatistics, Boston University, Boston, MA, 4Department of Biostatistics and 5Department of Biology, University of North Carolina at Chapel Hill, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph G.","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics, Illinois State University, Normal, IL, USA, 2Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany, 3Department of Biostatistics, Boston University, Boston, MA, 4Department of Biostatistics and 5Department of Biology, University of North Carolina at Chapel Hill, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Todd J.","family":"Vision","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics, Illinois State University, Normal, IL, USA, 2Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany, 3Department of Biostatistics, Boston University, Boston, MA, 4Department of Biostatistics and 5Department of Biology, University of North Carolina at Chapel Hill, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,1,15]]},"reference":[{"key":"2023013110114982900_B1","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1080\/10635150119889","article-title":"The phylogenetic trunk: maximal inclusion of taxa with missing data in an analysis of the lepospondyli","volume":"50","author":"Anderson","year":"2001","journal-title":"Syst. 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