A hierarchical model for incomplete alignments in phylogenetic inference Export

@article{citeulike:3891941, abstract = {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. 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. Availability: R code for fitting these models are available from: http://people.bu.edu/gupta/software.htm. Contact: gupta@bu.edu Supplementary information: Supplemantary data are available at Bioinformatics online. 10.1093/bioinformatics/btp015}, author = {Cheng, Fuxia and Hartmann, Stefanie and Gupta, Mayetri and Ibrahim, Joseph G. and Vision, Todd J.}, citeulike-article-id = {3891941}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp015}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/5/592}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19147663}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19147663}, day = {1}, doi = {10.1093/bioinformatics/btp015}, journal = {Bioinformatics}, keywords = {bayesian, distance-measures, phylogenetic-tree}, month = {March}, number = {5}, pages = {592--598}, posted-at = {2009-01-18 19:07:31}, priority = {2}, title = {A hierarchical model for incomplete alignments in phylogenetic inference}, url = {http://dx.doi.org/10.1093/bioinformatics/btp015}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:3891941 L3 - citeulike-article-id:3891941 N2 - 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. 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. Availability: R code for fitting these models are available from: http://people.bu.edu/gupta/software.htm. Contact: gupta@bu.edu Supplementary information: Supplemantary data are available at Bioinformatics online. 10.1093/bioinformatics/btp015 IS - 5 JF - Bioinformatics EP - 598 TI - A hierarchical model for incomplete alignments in phylogenetic inference VL - 25 SP - 592 KW - bayesian KW - distance-measures KW - phylogenetic-tree AU - Cheng, Fuxia AU - Hartmann, Stefanie AU - Gupta, Mayetri AU - Ibrahim, Joseph AU - Vision, Todd PY - 2009/03/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp015 ER -