From copair hypergraphs to median graphs with latent vertices
Discrete Mathematics
On weighted multiway cuts in trees
Mathematical Programming: Series A and B
Discrete Mathematics - Algebraic and topological methods in graph theory
Efficiently finding the most parsimonious phylogenetic tree via linear programming
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Certification of an optimal TSP tour through 85,900 cities
Operations Research Letters
Hi-index | 0.00 |
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.