Algorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction in Theory and Practice

Authors:
Srinath Sridhar;Kedar Dhamdhere;Guy Blelloch;Eran Halperin;R. Ravi;Russell Schwartz
Affiliations:
-;-;-;-;-;-
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2007

Citing 9
Cited 2

A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed

SIAM Journal on Computing
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
The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs

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Two Strikes Against Perfect Phylogeny

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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
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

Generalizing the four gamete condition and splits equivalence theorem: perfect phylogeny on three state characters

WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
The binary perfect phylogeny with persistent characters

Theoretical Computer Science

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Abstract

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 of additional mutations. We develop two algorithms for constructing optimal near-perfect phylogenies and provide empirical evidence of their performance. The first simple algorithm is fixed parameter tractable when the number of additional mutations and the number of characters that share four gametes with some other character are constants. The second, more involved algorithm for the problem is fixed parameter tractable when only the number of additional mutations is fixed. We have implemented both algorithms and shown them to be extremely efficient in practice on biologically significant data sets. This work proves the BNPP problem fixed parameter tractable and provides the first practical phylogenetic tree reconstruction algorithms that find guaranteed optimal solutions while being easily implemented and computationally feasible for data sets of biologically meaningful size and complexity.