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.
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Received: 25 May 1998 / Accepted: 8 December 1998
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Mitchison, G. A Probabilistic Treatment of Phylogeny and Sequence Alignment. J Mol Evol 49, 11–22 (1999). https://doi.org/10.1007/PL00006524
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DOI: https://doi.org/10.1007/PL00006524