TY - GEN

T1 - Simple reconstruction of binary near-perfect phylogenetic trees

AU - Sridhar, Srinath

AU - Dhamdhere, Kedar

AU - Blelloch, Guy E.

AU - Halperin, Eran

AU - Ravi, R.

AU - Schwartz, Russell

PY - 2006

Y1 - 2006

N2 - 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((72κ)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 worstcase 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.

AB - 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((72κ)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 worstcase 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.

UR - http://www.scopus.com/inward/record.url?scp=33746613585&partnerID=8YFLogxK

U2 - 10.1007/11758525_107

DO - 10.1007/11758525_107

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AN - SCOPUS:33746613585

SN - 3540343814

SN - 9783540343813

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 799

EP - 806

BT - Computational Science - ICCS 2006

PB - Springer Verlag

T2 - ICCS 2006: 6th International Conference on Computational Science

Y2 - 28 May 2006 through 31 May 2006

ER -