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
Theoretical Computer Science
Two Strikes Against Perfect Phylogeny
ICALP '92 Proceedings of the 19th International Colloquium on Automata, Languages and Programming
Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
A Polynomial-Time Algorithm for Near-Perfect Phylogeny
SIAM Journal on Computing
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
Parameterized Complexity
Fourier meets möbius: fast subset convolution
Proceedings of the thirty-ninth annual ACM symposium on Theory of computing
Algorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction in Theory and Practice
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Faster Steiner Tree Computation in Polynomial-Space
ESA '08 Proceedings of the 16th annual European symposium on Algorithms
Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficiently finding the most parsimonious phylogenetic tree via linear programming
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
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We consider the problem of finding a Steiner minimum tree in a hypercube. Specifically, given n terminal vertices in an m dimensional cube and a parameter q, we compute the Steiner minimum tree in time O(72q + 8qnm2), under the assumption that the length of the minimum Steiner tree is at most m + q. This problem has extensive applications in taxonomy and biology. The Steiner tree problem in hypercubes is equivalent to the phylogeny (evolutionary tree) reconstruction problem under the maximum parsimony criterion, when each taxon is defined over binary states. The taxa, character set and mutation of a phylogeny correspond to terminal vertices, dimensions and traversal of a dimension in a Steiner tree. Phylogenetic trees that mutate each character exactly once are called perfect phylogenies and their size is bounded by the number of characters. When a perfect phylogeny consistent with the data set exists it can be constructed in linear time. However, real data sets often do not admit perfect phylogenies. In this paper, we consider the problem of reconstructing near-perfect phylogenetic trees (referred to as BNPP). A near-perfect phylogeny relaxes the perfect phylogeny assumption by allowing at most q additional mutations. We show for the first time that the BNPP problem is fixed parameter tractable (FPT) and significantly improve the previous asymptotic bounds.