Construction of Phylogenetic Trees on Parallel Clusters
In this work, we present the preliminary step of a novel approach for the construction of phylogenetic trees on large parallel clusters of PCs. Computation of multiple alignments of biological sequences and phylogenetic tree construction are performed simultaneously. Any algorithm built upon this process uses the concept of neighborhood (which can be informally defined as sets of evolutionary related sequences). The process, called PhylTre, schematically consists in three iterative steps: the first step produces an undirected graph from a pre-processing operation. The second step aims at determining a neighborhood for each sequence. The third step builds partial phylogenetic trees using results stemmed from step two. The steps are applied iteratively until the whole phylogenetic tree is obtained.
A sequential code is available and it is currently implemented in parallel on a large cluster of PCs available at ID-IMAG.
KeywordsPhylogenetic Tree Minimum Span Tree Phylogenetic Tree Construction Parallel Cluster Perfect Phylogeny
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- [BEPT00]J. Blazewicz, K. Ecker, B. Plateau, and D. Trystram, editors. Handbook on Parallel and Distributed Processing. Internation Handbooks on Information Systems. Springer-Verlag, feb 2000.Google Scholar
- [Cha01]SuperTree Challenge. Goal: build a phylogenetic tree from more than 1000 phylogenies containing more than 11,000 taxa. http://www.life.umd.edu/labs/delwiche/deepgreen/DGchallenges.html, June 2001.
- [Csu01]M. Csürös. Fast recovery of evolutionary trees with thousands of nodes. In RECOMB 2001. Fifth Annual International Conference on Computational Molecular Biology, Montréal, Canada, april 22–25 2001.Google Scholar
- [dp01]Ribosomal database project. Ribosome data related services. http://rdp.cme.msu.edu/html/, June2001.
- [Fel73b]J. Felsenstein. Maximum likelihood estimation of evolutionary trees from continuous characters. Society of Human Genetics, 25:471–492, 1973.Google Scholar
- [Fel01]PHYLIP (J. Felsenstein). A free package for inferring phylogenies. Dept of Genetics, University of Washington. http://evolution.genetics.washington.edu/phylip.html, June 2001.
- [Gen01]Genbank. Nih genetic sequence database. http://www.ncbi.nlm.nih.gov, April 2001.
- [JY95]J. Jones and K. Yelick. Parallelizing the phylogeny problem. In Super-computing (SC’95), dec. 3–8, San Diego (USA), 1995.Google Scholar
- [MWWW01]B. Moret, L.-S. Wang, T. Warnow, and S. Wyman. New approaches for reconstructing phylogenies from gene order data. In Intelligent Systems for Molecular Biology (ISMB’01), Copenhagen, Denmark, 22–25 july 2001.Google Scholar
- [OMHO94]G. Olsen, H. Matsuda, R. Hagstrom, and R. Overbeek. fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Computer Applications in the Biosciences (CABIOS), 10:41–48, 1994.Google Scholar
- [Pol89]D. Polychronopoulos. Static and Dynamic Loop Scheduling. In Parallel Programming and Compilers. Kluwer Academic Publishers, 1989.Google Scholar
- [pp01]Green plant phylogeny. Goal: reconstruct the evolutionary relationships among all green plants. http://ucjeps.berkeley.edu/bryolab/GPphylo/GPproject.html, June 2001.
- [STB+99]_C. Stewart, T. Tan, M. Buchhorn, D. Hart, D. Berry, L. Zhang, E. Wern-ert, M. Sakharkarand W. Fisher, and D. McMullen. Evolutionary biology and computational grids. In IBM CASCON 1999 Computational Biology Workshop: Software Tools for Computational Biology, 1999.Google Scholar
- [Tre01]TreeBASE. A relational database of phylogenetic information. http://www.herbaria.harvard.edu/treebase, June 2001.
- [TSZC94]O. Trelles-Salazar, E. L. Zapata, and J.-M. Carazo. Mapping strategies for sequential sequence comparison algorithms on LAN-bases message passing architectures. In High Performance Computing and Networking’ 94, volume 796 of Lecture Notes in Computer Science (LNCS), pages 197–202. Springer-Verlag, Berlin, 1994.CrossRefGoogle Scholar
- [VAea01]C. Venter, M. Adams, and E. Myers et al. The sequence of the human genome. Science Magazine, 291, 2001.Google Scholar
- [YMFM95]T. K. Yap, P. J. Munson, O. Frieder, and R. L. Martino. Parallel multiple sequence alignment using speculative computation. In Internation Conference on Parallel Processing (ICPP’95), 1995.Google Scholar