Cooperative Rec-I-DCM3: A Population-Based Approach for Reconstructing Phylogenies

In this paper, we study the use of cooperation as a technique for designing faster algorithms for reconstructing phylogenetic trees. Our focus is on the use of cooperation to reconstruct trees based on maximum parsimony. Our baseline algorithm is Rec-I-DCM3, the best-performing MP algorithm known-to-date. Our results demonstrate that cooperation does improve the performance of the baseline algorithm by at least an order of magnitude in terms of running time. The use of cooperation also established a new best known score on one of our datasets.

[1]  W. Fitch.  Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .

[2]  Bernard M. E. Moret,et al.  Rec-I-DCM3: a fast algorithmic technique for reconstructing phylogenetic trees , 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

[3]  K. Nixon,et al.  The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis , 1999, Cladistics : the international journal of the Willi Hennig Society.

[4]  Hideo Matsuda,et al.  fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood , 1994, Comput. Appl. Biosci..

[5]  Tandy J. Warnow,et al.  Designing fast converging phylogenetic methods , 2001, ISMB.

[6]  Matthew J. Brauer,et al.  Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. , 2002, Molecular biology and evolution.

[7]  Pablo Moscato,et al.  On Evolution, Search, Optimization, Genetic Algorithms and Martial Arts : Towards Memetic Algorithms , 1989 .

[8]  Bernard M. E. Moret,et al.  Performance of Supertree Methods on Various Data Set Decompositions , 2004 .

[9]  David Gelernter,et al.  Generative communication in Linda , 1985, TOPL.

[10]  A. Lemmon,et al.  The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Clare Bates Congdon.  Gaphyl: An Evolutionary Algorithms Approach For The Study Of Natural Evolution , 2002, GECCO.

[12]  David A. Bader,et al.  Industrial applications of high-performance computing for phylogeny reconstruction , 2001, SPIE ITCom.

[13]  Tandy Warnow,et al.  Algorithmic techniques for improving the speed and accuracy of phylogenetic methods , 2004 .

[14]  K. Johnson.  Taxon sampling and the phylogenetic position of Passeriformes: evidence from 916 avian cytochrome b sequences. , 2001, Systematic biology.

[15]  D. Maddison.  The discovery and importance of multiple islands of most , 1991 .

[16]  O. Bininda-Emonds.  Phylogenetic Supertrees: Combining Information To Reveal The Tree Of Life , 2004 .

[17]  David P. Mindell,et al.  Molecular evidence of HIV-1 transmission in a criminal case , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Daniel H. Huson,et al.  Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction , 1999, J. Comput. Biol..

[19]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[20]  Daniel H. Huson,et al.  Solving Large Scale Phylogenetic Problems using DCM2 , 1999, ISMB.

[21]  Tandy J. Warnow,et al.  Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees , 2004, IEEE Computer Society Computational Systems Bioinformatics Conference.

[22]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[23]  Michael J. Sanderson,et al.  The Growth of Phylogenetic Information and the Need for a Phylogenetic Data Base , 1993 .

[24]  R. Graham,et al.  The steiner problem in phylogeny is NP-complete , 1982 .