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Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):4041-7. doi: 10.1098/rstb.2008.0140.

The impact of single substitutions on multiple sequence alignments.

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Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University Vienna, Veterinary University Vienna, Max F. Perutz Laboratories, Dr Bohrgasse 9, 1030 Wien, Austria.


We introduce another view of sequence evolution. Contrary to other approaches, we model the substitution process in two steps. First we assume (arbitrary) scaled branch lengths on a given phylogenetic tree. Second we allocate a Poisson distributed number of substitutions on the branches. The probability to place a mutation on a branch is proportional to its relative branch length. More importantly, the action of a single mutation on an alignment column is described by a doubly stochastic matrix, the so-called one-step mutation matrix. This matrix leads to analytical formulae for the posterior probability distribution of the number of substitutions for an alignment column.

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