title: A probabilistic treatment of phylogeny and sequence alignment.
abstract: Carrying out simultaneous tree-building and alignment of sequence data is a difficult computational task, and the methods currently available are either limited to a few sequences or restricted to highly simplified models of alignment and phylogeny. A method is given here for overcoming these limitations by Bayesian sampling of trees and alignments simultaneously. The method uses a standard substitution matrix model for residues together with a hidden Markov model structure that allows affine gap penalties. It escapes the heavy computational burdens of other models by using an approximation called the "*" rule, which replaces missing data by a sum over all possible values of variables. The behavior of the model is demonstrated on test sets of globins.
authors.affiliation: The Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK. gjm@mrc-lmb.cam.ac.uk
authors.forename: G J
authors.initials: GJ
authors.lastname: Mitchison
mesh_terms: D001499:Bayes Theorem; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D008390:Markov Chains; D008957:Models, Genetic; D010802:Phylogeny; D011336:Probability; D015983:Selection Bias; D016415:Sequence Alignment / Q000379:methods*; D017384:Sequence Deletion
chemical_list: D004251:DNA Transposable Elements