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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.

Author information

1
Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University Vienna, Veterinary University Vienna, Max F. Perutz Laboratories, Dr Bohrgasse 9, 1030 Wien, Austria. steffen.klaere@univie.ac.at

Abstract

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.

PMID:
18852110
PMCID:
PMC2607407
DOI:
10.1098/rstb.2008.0140
[Indexed for MEDLINE]
Free PMC Article

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