Optimized ancestral state reconstruction using Sankoff parsimony.

ABSTRACT:

Background

Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of changes required in a given phylogeny when a cost is associated to transitions between character states. Although optimizations exist to reduce the computations in the number of taxa, the original algorithm takes time O(n(2)) in the number of states, making it impractical for large values of n.

Results

In this study we introduce an optimization of Sankoff parsimony for the reconstruction of ancestral states when ultrametric or additive cost matrices are used. We analyzed its performance for randomly generated matrices, Jukes-Cantor and Kimura's two-parameter models of DNA evolution, and in the

SUBMITTER: Clemente JC 

PROVIDER: S-EPMC2677398 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature