%0 Journal Article
%T Probabilistic Phylogenetic Inference with Insertions and Deletions
%A Elena Rivas
%A Sean R. Eddy
%J PLOS Computational Biology
%D 2008
%I Public Library of Science (PLoS)
%R 10.1371/journal.pcbi.1000172
%X A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth¨Cdeath) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new ˇ°concordance testˇ± benchmark on real ribosomal RNA alignments, we show that the extended program dnaml¦Ĺ improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm.
%U http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000172