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
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
Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference
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
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
On the genealogy of asexual diploids
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
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We consider the problem of reconstructing near-perfect phylogenetic trees using binary character states (referred to as BNPP). A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree, yielding an algorithm for binary character states that is computationally efficient but not robust to imperfections in real data. A near-perfect phylogeny relaxes the perfect phylogeny assumption by allowing at most a constant number q of additional mutations. In this paper, we develop an algorithm for constructing optimal phylogenies and provide empirical evidence of its performance. The algorithm runs in time O((72 κ)qnm + nm2) where n is the number of taxa, m is the number of characters and κ is the number of characters that share four gametes with some other character. This is fixed parameter tractable when q and κ are constants and significantly improves on the previous asymptotic bounds by reducing the exponent to q. Furthermore, the complexity of the previous work makes it impractical and in fact no known implementation of it exists. We implement our algorithm and demonstrate it on a selection of real data sets, showing that it substantially outperforms its worst-case bounds and yields far superior results to a commonly used heuristic method in at least one case. Our results therefore describe the first practical phylogenetic tree reconstruction algorithm that finds guaranteed optimal solutions while being easily implemented and computationally feasible for data sets of biologically meaningful size and complexity.