Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny

Biology – Quantitative Biology – Populations and Evolution

Scientific paper

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

15 pages

Scientific paper

Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast heuristic methods that are empirically known to work very well in general, but can yield results arbitrarily far from optimal. Practical exact methods, which yield exponential worst-case running times but generally much better times in practice, provide an important alternative. We report progress in this direction by introducing a provably optimal method for the weighted multi-state maximum parsimony phylogeny problem. The method is based on generalizing the notion of the Buneman graph, a construction key to efficient exact methods for binary sequences, so as to apply to sequences with arbitrary finite numbers of states with arbitrary state transition weights. We implement an integer linear programming (ILP) method for the multi-state problem using this generalized Buneman graph and demonstrate that the resulting method is able to solve data sets that are intractable by prior exact methods in run times comparable with popular heuristics. Our work provides the first method for provably optimal maximum parsimony phylogeny inference that is practical for multi-state data sets of more than a few characters.

No associations

LandOfFree

Say what you really think

Search LandOfFree.com for scientists and scientific papers. Rate them and share your experience with other people.

Rating

Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFWR-SCP-O-52113

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.