From copair hypergraphs to median graphs with latent vertices
Discrete Mathematics
A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies
SIAM Journal on Computing
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
A Polynomial-Time Algorithm for Near-Perfect Phylogeny
SIAM Journal on Computing
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Fixed parameter tractability of binary near-perfect phylogenetic tree reconstruction
ICALP'06 Proceedings of the 33rd international conference on Automata, Languages and Programming - Volume Part I
A fundamental decomposition theory for phylogenetic networks and incompatible characters
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Simple reconstruction of binary near-perfect phylogenetic trees
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Genome-wide compatible SNP intervals and their properties
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
On the genealogy of asexual diploids
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Generalized buneman pruning for inferring the most parsimonious multi-state phylogeny
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Blocks and Cut Vertices of the Buneman Graph
SIAM Journal on Discrete Mathematics
Hi-index | 0.00 |
Reconstruction of phylogenetic trees is a fundamental problem in computational biology. While excellent heuristic methods are available for many variants of this problem, new advances in phylogeny inference will be required if we are to be able to continue to make effective use of the rapidly growing stores of variation data now being gathered. In this paper, we introduce an integer linear programming formulation to find the most parsimonious phylogenetic tree from a set of binary variation data. The method uses a flow-based formulation that could use exponential numbers of variables and constraints in the worst case. The method has, however, proved extremely efficient in practice on datasets that are well beyond the reach of the available provably efficient methods. The program solves several large mtDNA and Y-chromosome instances within a few seconds, giving provably optimal results in times competitive with fast heuristics than cannot guarantee optimality.