A fast program for maximum likelihood-based inference of large phylogenetic trees

Proceedings of the ACM Symposium on Applied Computing

Volumn 1, Issue , 2004, Pages 197-201

  Stamatakis, A P ^a   Ludwig, T ^b   Meier, H ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

Maximum Likelihood; Parallel Distributed Computing; Phylogenetic Inference

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; FUNCTIONS; GENETIC ENGINEERING; MAXIMUM LIKELIHOOD ESTIMATION; PARALLEL PROCESSING SYSTEMS;

GENETIC INFORMATION; PARTIALLY RANDOMIZED ALGORITHMS; PHYLOGENETIC INFERENCE;

COMPUTER SOFTWARE;

EID: 2442484847     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/967900.967940     Document Type: Conference Paper

References (21)

1. M.J. Brauer et al. Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. In Molecular Biology and Evolution 19:1717-1726, 2002.
2. R.W. DeBry, L. G. Abele. The relationship between parsimony and maximum likelihood analyses: tree scores and confidence estimates. In Mol. Biol. Evol. 12:291-297, 1995.
3. J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach. In J. Mol Evol. 17:368-376, 1981.
4. P.A. Goloboff. Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima. In Cladistics 15:415-428, 1999.
5. HEidelberg Linux Cluster System: helics.uni-hd.de. Technical Information about the HELICS cluster.
6. J.P. Huelsenbeck, F. Ronquist. MRBAYES: Bayesian inference of phylogenetic trees. In Bioinformatics 17(8):754-5, 2001.
7. L.S. Jermiin et al. Majority-rule consensus of phylogenetic trees obtained by maximum-likelihood analysis. Mol. Biol. Evol. 14:1297-1302, 1997.
8. W. Ludwig et al. ARE: a software environment for sequence data. In Nucl. Acids Res., in press, 2003.
9. G.J. Olsen et al. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. In Comput. Appl. Biosci. 10:41-48, 1994.
10. parallel fastDNAml www.indiana.edu/~rac/hpc/fastDNAml. Download site including additional information results and test data.
11. PAxML/RAxML download site. wwwbode.in.tum.de/~staraatak/research.html
12. PHYLIP evolution.genetics.Washington.edu/phylip.htrnl. Downlaod site for PHYLIP version 3.5, version 3.6 alpha and related documentation.
13. RAxML@home development site. www.sourceforge.com/projects/axml
14. PAUP download and information site. paup.csit.fsu.edu
15. A.P.Stamatakis et al. Accelerating Parallel Maximum Likelihood-based Phylogenetic Tree Computations using Subtree Equality Vectors. In Proceedings of Supercomputing Conference (SC2002), Baltimore, Maryland, November 2002.
16. A.P.Stamatakis, T. Ludwig. Phylogenetic Tree Inference on PC Architectures with AxML/PAxML. In Proceedings of IPDPS2003, High Performance Computational Biology Workshop (HICOMB), Nice, France, April 2003.
17. C. A. Stewart et al. Parallel implementation and performance of fastDNAml - a program for maximum likelihood phylogenetic inference. In proceedings of SC2001, Denver, Colorado, November 2001.
18. K. Strimmer, A.v. Haeseler, Quartet Puzzling: A Maximum-Likelihood Method for Reconstructing Tree Topologies. In Mol. Biol. Evol 13:964-969, 1996.
19. C. Tuffley, M. Steel. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. In Bull Math Biol 59(3):581-607, 1997.
20. T.L. Williams, B.M.E. Moret. An Investigation of Phylogenetic Likelihood Methods. In Proceedings of 3rd IEEE Symposium, on Bioinformatics and Bioengineering (BIBE'O3), 2003.
21. M.J. Wolf et al. TrExML: A maximum likelihood program for extensive tree-space exploration. In Bioinformatics 16:383-394, 2000.