Incomparability of results between phylogeneticn search programs

Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008

Volumn , Issue , 2008, Pages 81-84

  Sundberg, Kenneth ^a   Carroll, Hyrum ^a   Snell, Quinn ^a   Clement, Mark ^a  

^a 3361 TMCB   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SCORING METHODS; SEARCH STRATEGIES;

BIOINFORMATICS;

EID: 62649109946     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. A.G. Clark, K.M. Weiss, D.A. Nickerson, S.L. Taylor, A. Buchanan, J. Stengard, V. Salomaa, E. Vartiainen, M. Perola, E. Boerwinkle, and C.F. Sing. Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. American Journal of Human Genetics, 63:595-612, 1998.
2. K.A. Crandall. Multiple interspecies transmissions of human and simian t-cell leukemia/lymphoma virus type i sequences. Molecular Biology and Evolution, 13:115-131, 1996.
3. R. DeSalle. Molecular approaches to biogeographic analysis of Hawaiian Drosophilidae. Hawaiian Biogeography (ed. by WL Wagner and VA Funk), pp. 72-89, 1995.
4. J. Felsenstein. Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters. Systematic Zoology, 22(3):240-249, 1973.
5. S. Guindon and O. Gascuel. A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology, 52(5):696-704, 2003.
6. S. Guindon, F. Lethiec, P. Duroux, and O. Gascuel. PHYML Onlinea web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res, 33(suppl 2):W557-W559, 2005.
7. M. Hasegawa, H. Kishino, and T. Yano. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22(2):160-174, 1985.
8. BL Herring, F. Bernardin, S. Caglioti, S. Stramer, L. Tobler, W. Andrews, L. Cheng, S. Rampersad, C. Cameron, J. Saldanha, et al. Phylogenetic analysis of WNV in North American blood donors during the 2003-2004 epidemic seasons. Virology, 2007.
9. T.H. Jukes and C.R. Cantor. Evolution of protein molecules. Mammalian Protein Metabolism, 3:21-132, 1969.
10. C. Lanave, G. Preparata, C. Sacone, and G. Serio. A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution, 20(1):86-93, 1984.
11. G.J. Olsen, H. Matsuda, R. Hagstrom, and R. Over-beek. fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Bioinformatics, 10(1):41-48, 2001.
12. F. Rodriguez, JL Oliver, A. Marin, and JR Medina. The general stochastic model of nucleotide substitution. J Theor Biol, 142(4):485-501, 1990.
13. C.F. Sing, M.B. Haviland, K.E. Zerba, and A.R. Templeton. Application of cladistics to the analysis of genotype-phenotype relationships. European Journal of Epidemiology, 8:3-9, 1992.
14. A. Stamatakis. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21):2688, 2006.
15. A. Stamatakis, T. Ludwig, and H. Meier. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21(4):456-463, 2005.
16. David L. Swofford. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts, 2003.
17. J. Thompson, F. Plewniak, and O. Poch. BAliBASE: A benchmark alignments database for the evaluation of multiple sequence alignment programs. Bioinformatics, 15(1):87-88, 1999.
18. Z. Yang. PAML: a program package for phylogenetic analysis by maximum likelihood, 2005.
19. D.J. Zwickl. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD thesis, The University of Texas at Austin, 2006.