Journal of Algorithms
Permuting matrices to avoid forbidden submatrices
Discrete Applied Mathematics - Special volume: Aridam VI and VII, Rutcor, New Brunswick, NJ, USA (1991 and 1992)
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies
SIAM Journal on Computing
STOC '98 Proceedings of the thirtieth annual ACM symposium on Theory of computing
Decremental dynamic connectivity
Journal of Algorithms
Two Strikes Against Perfect Phylogeny
ICALP '92 Proceedings of the 19th International Colloquium on Automata, Languages and Programming
COCOON '02 Proceedings of the 8th Annual International Conference on Computing and Combinatorics
On the Generality of Phylogenies from Incomplete Directed Characters
SWAT '02 Proceedings of the 8th Scandinavian Workshop on Algorithm Theory
| Hi-index | 0.00 |
Perfect phylogeny is one of the fundamental models for studying evolution. We investigate the following generalization of the problem: The input is a species-characters matrix. The characters are binary and directed, i.e., a species can only gain characters. The difference from standard perfect phylogeny is that for some species the state of some characters is unknown. The question is whether one can complete the missing states in a way admitting a perfect phylogeny. The problem arises in classical phylogenetic studies, when some states are missing or undetermined. Quite recently, studies that infer phylogenies using inserted repeat elements in DNA gave rise to the same problem. The best known algorithm for the problem requires O(n2m) time for m characters and n species. We provide a near optimal Õ(nm)-time algorithm for the problem.