MetaPIGA v2.0: Maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Helaers, Raphaël ^a   Milinkovitch, Michel C ^b  

^a UNIVERSITY OF NAMUR   (Belgium)

^b Sciences III   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

AKAIKE INFORMATION CRITERION; BAYESIAN INFORMATION CRITERION; COMMAND LINE PROCESSING; COMPARISON OF PERFORMANCE; COMPLEX SUBSTITUTIONS; LIKELIHOOD RATIO TESTS; PLATFORM INDEPENDENT; SIMULATED ANNEALING ALGORITHMS;

BIOLOGY; ERGONOMICS; GENETIC ALGORITHMS; GRAPHICAL USER INTERFACES; HEURISTIC ALGORITHMS; INFERENCE ENGINES; STATISTICAL TESTS; STOCHASTIC SYSTEMS;

STOCHASTIC MODELS;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGY; COMPUTER PROGRAM; INTERNET; METHODOLOGY; PHYLOGENY; STATISTICAL MODEL;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; INTERNET; LIKELIHOOD FUNCTIONS; PHYLOGENY; SOFTWARE;

EID: 77954562361     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-379     Document Type: Article

References (44)

1. Gabaldon T. Large-scale assignment of orthology: back to phylogenetics?. Genome Biol 2008, 9(10):235. 10.1186/gb-2008-9-10-235, 2760865, 18983710.
2. Li W-H. Molecular evolution. 1997, Sunderland, MA.: Sinauer.
3. Thorne JL, Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Syst Biol 2002, 51(5):689-702. 10.1080/10635150290102456, 12396584.
4. Cassens I, Vicario S, Waddell VG, Balchowsky H, Van Belle D, Ding W, Fan C, Mohan RS, Simoes-Lopes PC, Bastida R, et al. Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages. Proc Natl Acad Sci USA 2000, 97(21):11343-11347. 10.1073/pnas.97.21.11343, 17202, 11027333.
5. Thorne JL, Kishino H, Painter IS. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 1998, 15(12):1647-1657.
6. Blanchette M, Green ED, Miller W, Haussler D. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res 2004, 14(12):2412-2423. 10.1101/gr.2800104, 534665, 15574820.
7. Chang BS, Jonsson K, Kazmi MA, Donoghue MJ, Sakmar TP. Recreating a functional ancestral archosaur visual pigment. Molecular biology and evolution 2002, 19(9):1483-1489.
8. Chang BS, Ugalde JA, Matz MV. Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins. Methods Enzymol 2005, 395:652-670. full_text, 15865989.
9. Williams PD, Pollock DD, Blackburne BP, Goldstein RA. Assessing the accuracy of ancestral protein reconstruction methods. PLoS computational biology 2006, 2(6):e69. 10.1371/journal.pcbi.0020069, 1480538,1480538, 16789817.
10. Zhang J, Nielsen R, Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular biology and evolution 2005, 22(12):2472-2479. 10.1093/molbev/msi237, 16107592.
11. Meegaskumbura M, Bossuyt F, Pethiyagoda R, Manamendra-Arachchi K, Bahir M, Milinkovitch MC, Schneider CJ. Sri Lanka: an amphibian hot spot. Science 2002, 298(5592):379. 10.1126/science.298.5592.379, 12376694.
12. Springer MS, Stanhope MJ, Madsen O, de Jong WW. Molecules consolidate the placental mammal tree. Trends in ecology & evolution (Personal edition) 2004, 19(8):430-438.
13. Bossuyt F, Brown RM, Hillis DM, Cannatella DC, Milinkovitch MC. Phylogeny and biogeography of a cosmopolitan frog radiation: Late cretaceous diversification resulted in continent-scale endemism in the family ranidae. Syst Biol 2006, 55(4):579-594. 10.1080/10635150600812551, 16857652.
14. Graham RL, Foulds LR. Unlikelihood that Minimal Phylogenies for a Realistic Biological Study Can Be Constructed in Reasonable Computational Time. Math Bioscience 1982, 60:133-142.
15. Chor B, Tuller T. Maximum likelihood of evolutionary trees: hardness and approximation. Bioinformatics 2005, 21(Suppl 1):i97-106. 10.1093/bioinformatics/bti1027, 15961504.
16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of molecular evolution 1981, 17:368-376. 10.1007/BF01734359, 7288891.
17. Felsenstein J. Inferring Phylogenies. 2004, Sunderland: Sinauer Associates Inc.
18. Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst Biol 2001, 50(4):525-539. 10.1080/106351501750435086, 12116651.
19. Holder M, Lewis PO. Phylogeny estimation: traditional and Bayesian approaches. Nat Rev Genet 2003, 4(4):275-284. 10.1038/nrg1044, 12671658.
20. Huelsenbeck JP, Larget B, Miller RE, Ronquist F. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst Biol 2002, 51(5):673-688. 10.1080/10635150290102366, 12396583.
21. Salter LA, Pearl DK. Stochastic search strategy for estimation of maximum likelihood phylogenetic trees. Syst Biol 2001, 50(1):7-17. 10.1080/106351501750107413, 12116596.
22. Katoh K, Kuma K, Miyata T. Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny. J Mol Evol 2001, 53(4-5):477-484. 10.1007/s002390010238, 11675608.
23. Lemmon AR, Milinkovitch MC. The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation. Proc Natl Acad Sci USA 2002, 99(16):10516-10521. 10.1073/pnas.162224399, 124960, 12142465.
24. Lewis PO. A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Mol biol evol 1998, 15(3):277-283.
25. Matsuda H. Protein phylogenetic inference using maximum likelihood with a genetic algorithm. Pacific symposium on biocomputing '96 1996, 512-523. London: World Scientific.
26. Zwickl DJ. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. 2006, Austin, Tx, USA.: The University of Texas.
27. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19(12):1572-1574. 10.1093/bioinformatics/btg180, 12912839.
28. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688-2690. 10.1093/bioinformatics/btl446, 16928733.
29. Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenetics. Bioinformatics 2009, 25(11):1370-1376. 10.1093/bioinformatics/btp244, 2682525, 19369496.
30. Tavaré S. Some Probabilistic and Statistical Problems in the Analysis of DNA Sequences. American Mathematical Society: Lectures on Mathematics in the Life Sciences 1986, 17:57-86.
31. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 1994, 39(3):306-314. 10.1007/BF00160154, 7932792.
32. Yang Z. Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology & Evolution 1996, 11(9):367-372.
33. Gu X, Fu YX, Li WH. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol biol evol 1995, 12(4):546-557.
34. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52(5):696-704. 10.1080/10635150390235520, 14530136.
35. Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005, 21(4):456-463. 10.1093/bioinformatics/bti191, 15608047.
36. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 1987, 4(4):406-425.
37. Felsenstein J. Inferring Phylogenies. 2002, Sunderland: Sinauer Associates Inc.
38. Zwickl DJ. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. 2006, Austin, TX, USA.: The University of Texas.
39. Kirkpatrick S, Gelatt CD, Vecchi MP. Optimization by Simulated Annealing. Science 1983, 220(4598):671-680. 10.1126/science.220.4598.671, 17813860.
40. Lundy M. Applications of the Annealing Algorithm to Combinatorial Problems in Statistics. Biometrika 1985, 72(1):191-198.
41. Holland J. Adaptation in Natural and Artificial Systems. 1975, Ann Arbor: University of Michigan Press.
42. Maddison DR, Swofford DL, Maddison WP. NEXUS: an extensible file format for systematic information. Syst Biol 1997, 46(4):590-621.
43. Posada D, Crandall KA. Selecting the best-fit model of nucleotide substitution. Syst Biol 2001, 50(4):580-601. 10.1080/106351501750435121, 12116655.
44. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010, 59(3):307-321. 10.1093/sysbio/syq010, 20525638.