Optimized ancestral state reconstruction using Sankoff parsimony |
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| Authors: | José C Clemente Kazuho Ikeo Gabriel Valiente Takashi Gojobori |
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| Affiliation: | (1) Center for Information Biology and DNA Databank of Japan, National Institute of Genetics, Yata 1111, Mishima, Japan;(2) Technical University of Catalonia, E-08034 Barcelona, Spain |
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| 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. |
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