%0 Journal Article %1 klaere2008 %A Klaere, Steffen %A Gesell, Tanja %A von Haeseler, Arndt %D 2008 %J Philosophical Transactions of the Royal Society B %K maximum_likelihood maximum_parsimony posterior_probability substitution_model tree_reconstruction %N 1512 %P 4041-4047 %T The impact of single substitutions on multiple sequence alignments %U http://dx.doi.org/10.1098/rstb.2008.0140 %V 363 %X 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.

@article{klaere2008, 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.}, added-at = {2009-05-14T23:36:57.000+0200}, author = {Klaere, Steffen and Gesell, Tanja and von Haeseler, Arndt}, biburl = {https://www.bibsonomy.org/bibtex/2257a63852a083f64ef0f6db76abd240d/compevol}, interhash = {a3932211cf8ba466ddaf1e912b7b1a51}, intrahash = {257a63852a083f64ef0f6db76abd240d}, journal = {Philosophical Transactions of the Royal Society B}, keywords = {maximum_likelihood maximum_parsimony posterior_probability substitution_model tree_reconstruction}, month = Dec, number = 1512, pages = {4041-4047}, timestamp = {2009-05-14T23:36:57.000+0200}, title = {The impact of single substitutions on multiple sequence alignments}, url = {http://dx.doi.org/10.1098/rstb.2008.0140}, volume = 363, year = 2008 }