Pathological rate matrices: from primates to pathogens.

ABSTRACT:

Background

Continuous-time Markov models allow flexible, parametrically succinct descriptions of sequence divergence. Non-reversible forms of these models are more biologically realistic but are challenging to develop. The instantaneous rate matrices defined for these models are typically transformed into substitution probability matrices using a matrix exponentiation algorithm that employs eigendecomposition, but this algorithm has characteristic vulnerabilities that lead to significant errors when a rate matrix possesses certain 'pathological' properties. Here we tested whether pathological rate matrices exist in nature, and consider the suitability of different algorithms to their computation.

Results

We used concatenated protein coding gene alignments from microbial geno

SUBMITTER: Schranz HW 

PROVIDER: S-EPMC2639438 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature