IQPNNI: Moving fast through tree space and stopping in time

Molecular Biology and Evolution

Volumn 21, Issue 8, 2004, Pages 1565-1571

  Vinh, Le Sy ^a   Von Haeseler, Arndt ^a,b  

^a HEINRICH HEINE UNIVERSITY   (Germany)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

Accuracy; Maximum likelihood; Nearest neighbor interchange; Phylogenetics; Quartet tree; rbcL; Record value; Sequence evolution; Tree reconstruction

Indexed keywords

RIBOSOME RNA;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; DNA SEQUENCE; PHYLOGENETIC TREE CONSTRUCTION METHOD; RNA SEQUENCE; SIMULATION;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; HUMANS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 3242801484     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh176     Document Type: Article

References (29)

1. Brauer, M. J., M. T. Holder, L. A. Dries, D. J. Zwickl, P. L. O. Lewis, and D. M. Hillis. 2002. Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. Mol. Biol. Evol. 19:1717-1726.
2. Bruno, W. J., N. D. Socci, and A. L. Halpern. 2000. Weighted Neighbor Joining: a likelihood-based approach to distance-based phylogeny reconstruction. J. Mol. Evol. 17:189-197.
3. Charleston, M. A. 2001. Hitch-hiking: a parallel heuristic search strategy, applied to the phylogeny problem. J. Comput. Biol. 8:79-91.
4. Cooke, P. 1980. Optimal linear estimation of bounds of random variables. Biometrika 67:257-258.
5. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington, Seattle. Distributed by the author.
6. -. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, Mass.
7. Gascuel, O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14:685-695.
8. Guindon, S., and O. Gascuel. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
9. Harding, E. F. 1971. The probabilities of rooted tree-shapes generated by random bifurcation. Adv. Appl. Prob 3:44-77.
10. Hasegawa, M., H. Kishino, and T.-A. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
11. Huson, D. H., S. M. Nettles, and T. J. Warnow. 1999. Disk-covering, a fast-converging method for phylogenetic reconstruction. J. Comput. Biol. 6:369-386.
12. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
13. Larget, B. and D. L. Simon. 1999. Markov chain Monte Carlo alogorithms for the Bayesian of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
14. Lemmon, A. R., and M. C. Milinkovitch. 2002. The metapopulation genetic algorithm: an efficient solution for the problem of large phylogeny estimation. Proc. Natl. Acad. Sci. USA 99:10516-10521.
15. Olsen, G. J., H. Matsuda, R. Hagstrom, and R. Overbeek. 1994. fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10:41-48.
16. Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
17. Ranwez, V., and O. Gascuel. 2001. Quartet-based phylogenetic inference: improvements and limits. Mol. Biol. Evol. 18:1103-1116.
18. Robert, D. L., and A. R. Solow. 2003. When did the dodo become extinct? Nature 426:245-245.
19. Robinson, D. R., and L. R. Foulds. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
20. Ronquist, F., and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
21. Saitou, N., and M. Nei. 1987. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
22. Schmidt, H. A. 2003. Phylogenetic trees from large datasets. Ph.D. thesis, Universität Düsseldorf.
23. Schmidt, H. A., and A. von Haeseler. 2002. Quartet trees as a tool to reconstruct large trees from sequences. Pp. 379-388 in K. Jajuga, A. Sokolowski, and H.-H. Bock, eds., Data analysis, classification, and related methods. Studies in classification, data analysis, and knowledge organization. Springer-Verlag, Heidelberg, New York.
24. Schmidt, H. A., E. Petzold, M. Vingron, and A. von Haeseler. 2003. Molecular phylogenetics: parallelized parameter estimation and quartet puzzling. J. Parallel Distrib. Comput. 63:719-727.
25. Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
26. Strimmer, K. and A. von Haeseler. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
27. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogeny reconstruction. Pp. 407-514 in D. M. Hillis, C. Moritz, and B. K. Mable, eds., Molecular Systematics, 2nd edition. Sinauer Associates, Sunderland, Mass.
28. Vos, R. 2003. Accelerated likelihood surface exploration: the likelihood ratchet. Syst. Biol 52:368-373.
29. Willson, S. J. 1999. Building phylogenetic trees from quartets by using local inconsistency measures. Mol. Biol. Evol. 16:685-693.