Evolutionary distances in the twilight zone--a rational kernel approach.

ABSTRACT: Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers

SUBMITTER: Schwarz RF 

PROVIDER: S-EPMC3013127 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature