Result verification, code verification and computation of support values in phylogenetics

Briefings in Bioinformatics

Volumn 12, Issue 3, 2011, Pages 270-279

  Stamatakis, Alexandros ^a   Izquierdo Carrasco, Fernando ^a,b  

^a HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

^b HITS   (Germany)

Author keywords

Bootstrap; Maximum likelihood; Phylogenetics; Program verification; Software bug; Support values

Indexed keywords

ARTICLE; COMPUTER SIMULATION; GENETIC DATABASE; MOLECULAR EVOLUTION; PHYLOGENY;

COMPUTER SIMULATION; DATABASES, GENETIC; EVOLUTION, MOLECULAR; PHYLOGENY;

EID: 79955748361     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbq079     Document Type: Article

References (86)

1. Camin JH, Sokal RR. A method for deducing branching sequences in phylogeny. Evolution 1965;19:311-26.
2. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969;18:1-32.
3. Kunin V, Goldovsky L, Darzentas N, et al. The net of life: Reconstructing the microbial phylogenetic network. Genome Res 2005;15:954-9.
4. Creevey CJ, Fitzpatrick DA, Philip GK, et al. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc RSoc Lond B 2004;271(1557):2551-8.
5. Cavalli-Sforza LL, Edwards AWF. Phylogenetic analysis: models and estimation procedures. Evolution 1967;21: 550-70.
6. Farris JS. Methods for computing Wagner trees. Syst Zool 1970;18:374-85.
7. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17(6): 368-76.
8. Foulds LR, Graham RL. The Steiner problem in phylogeny is NP-complete. AdvApplMath 1982;3:43-9.
9. Roch S. A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. IEEE/ACMTrans Comput Biol Bioinform 2006;3(1):92-4.
10. Goloboff PA. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 1999;15(4): 415-28.
11. Stamatakis A. RAxML-VI: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006;22(21):2688-90.
12. Zwickl D. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD diss., The University of Texas at Austin, 2006.
13. Guindon S, Dufayard JF, Lefort V, et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59(3):307-21.
14. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003; 19(12):1572-4.
15. Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009;25(17):2286-8.
16. Wiens JJ. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst Biol 1998;47(4): 625-40.
17. Hillis DM, Huelsenbeck JP, Cunningham CW. Application and accuracy of molecular phylogenies. Science 1994; 264(5159):671-7.
18. Strimmer K, von Haeseler A. Accuracy of neighbor joining for n-taxon trees. Syst Biol 1996;45(4):516-23.
19. Yang Z. Phylogenetic analysis using parsimony and likelihood methods. J Mol Evol 1996;42(4):294-307.
20. Guindon S, Gascuel O. A simple, fast, and accurate method to estimate large phylogenies by maximum likelihood. Syst Biol 2003;52(5):696-704.
21. Zwickl DJ, Hillis DM. Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 2002;51(4): 588-98.
22. Nei M, Kumar S, Takahashi K. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. ProcNatl Acad SciUSA 1998;95(21):12390-7.
23. Hillis DM. Approaches for Assessing Phylogenetic Accuracy. Syst Biol 1995;44(1):3-16.
24. Huelsenbeck JP, Lander KM. Frequent inconsistency of parsimony under a simple model of cladogenesis. Syst Biol 2003;52(5):641-8.
25. Rambaut A, Grass NC. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Bioinformatics 1997;13(3):235-8.
26. Fletcher W, Yang Z. INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol 2009;26(8): 1879-88.
27. Cartwright RA. DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics 2005;21:iii31-8.
28. Puigbo P, Garcia-Vallve S, McInerney JO. TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics 2007;23(12):1556-8.
29. Ripplinger J, Sullivan J. Does choice in model selection affect maximum likelihood analysis? Syst Biol 2008;57(1): 76-85.
30. Lanave C, Preparata G, Saccone C, et al. A new method for calculating evolutionary substitution rates. J Mol Evol 1984; 20:86-93.
31. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 1994;39(3):306-14.
32. Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005;21(4):456-63.
33. Joe Felsenstein. Inferring Phylogenies pp 269-274 Sinaur Associates Inc. 2004.
34. Ogden TH, Rosenberg MS. Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol 2006;55(2): 314-28.
35. Redlings BD, Suchard M. Joint Bayesian estimation of alignment and phylogeny. Syst Biol 2005;54(3):401-18.
36. Löytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 2008;320(5883):1632-5.
37. Fleissner R, Metzler D, von Haeseler A. Simultaneous statistical multiple alignment and phylogeny reconstruction. Syst Biol 2005;54(4):548-61.
38. Sennbald B, Lagergren J. Probabilistic orthology analysis. Syst Biol 2009;58(4):411-24.
39. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. GenomeRes 2003; 13(9):2178-89.
40. Smith SA, Beaulieu J, Donoghue MJ. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol Biol 2009;9:37.
41. Hartmann S, Vision TJ. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol 2008;8:95.
42. Maddison PW. Gene trees in species trees. Syst Biol 1997; 46(3):523-36.
43. Degnan JH, Rosenberg NA. Discordance of species trees with their most likely gene trees. Plos Genetics 2006;2(5): e68.
44. Hill AW, Guralnick RP, Wilson MJC, et al. Evolution of drug resistance in multiple distinct lineages of H5N1 avian influenza. Infect Genet Evol 2009;9:169-78.
45. Salzberg SL, Kingsford C, Cattoli G, et al. Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses. Emerg Infect Dis 2007;13(5):713-8.
46. Larget B, Simon DL. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 1999;16(6):750-9.
47. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783-91.
48. Anisimova M, Gascuel O. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol 2006;55(4):539-55.
49. Stuart A, Ord JK, Arnold S. Kendall's advanced theory of statistics. New York: Oxford University Press, 1999.
50. Li S. Phylogenetic reconstruction using Markov chain Monte Carlo. PhD diss. Columbus: The Ohio State University, 1996.
51. Swofford DL, Olsen GJ, Waddell PJ, et al. Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK, (eds). Molecular Systematics. Sunderland, Massachusetts: Sinauer Associates, 1996;407-514.
52. Siddall ME. Measures of support. In: DeSalle R, Giribet G, Wheeler W, (eds). Techniques in Molecular Systematics and Evolution. Basel: Birkhäuser Verlag, 2002;80-101.
53. Efron B. Bootstrapping methods: another look at the jackknife. Ann Stat 1979;7(1):1-26.
54. Hedges BS. The number of replicates needed for accurate estimation of the bootstrap p value in phylogenetic studies. Mol Biol Evol 1992;9(2):366-9.
55. Pattengale ND, Alipour M, Bininda-Emonds ORP, et al. How many bootstrap replicates are necessary? J Comput Biol 2010;17(3):337-54.
56. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PloS ONE 2010;5(3):e9490.
57. Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999;16:1114-6.
58. Susko E. Bootstrap support is not first-order correct. Syst Biol 2009;58(2):211-23.
59. Susko E. First-order correct bootstrap support adjustments for splits that allow hypothesis testing when using maximum likelihood estimation. Mol Biol Evol 2010;27(7):1621-9.
60. Metropolis N, Rosenbluth AW, Rosenbluth MN, et al. Equation of state calculations by fast computing machines. JChemPhys 1953;21:1087-92.
61. Hastings WK. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 1970;57: 97-109.
62. Nylander JAA, Wilgenbusch JC, Warren DL, et al. AWTY(are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008;24(4):581-3.
63. Yang Z. Fair-balance paradox, star-tree paradox, and bayesian phylogenetics. Mol Biol Evol 2007;24(8):1639-55.
64. Pagel A, Meade A. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst Biol 2004;53(4):571-81.
65. Lartillot N, Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 2004;21(5):1095-109.
66. Wang HC, Li K, Susko E, Roger AJ. A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. BMC Evol Biol 2008;8(1):331.
67. Kolaczkowski B, Thornton JW. A mixed branch length model of heterotachy improves phylogenetic accuracy. Mol Biol Evol 2008;25(6):1054-66.
68. Casella G, George EI. Explaining the Gibbs sampler. Am Stat 1992;46(3):167-74.
69. Green PJ. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 1995;82(4):711-32.
70. Douady CJ, Delsuc F, Boucher Y, et al. Comparison of bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol Biol Evol 2003;20(2):248-54.
71. Alfaro ME, Zoller S, Lutzoni F. Bayes or bootstrap? A simulation study comparing the performance of bayesian markov chain monte carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol 2003;20(2):255-66.
72. Wilcox TP, Zwickl DJ, Heath TA, et al. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol Phylogenet Evol 2002;25(2):361-71.
73. Hillis DM, Bull JJ. An empirical test of bootstrapping as a method for assesing confidence in phylogenetic analysis. Syst Biol 1993;42(2):182-92.
74. Henzinger TA, Jhala R, Majumdar R, et al. Software verification with BLAST. In: Proceedings of the 10th International Conference on Model Checking Software. Berlin/Heidelberg, New York: Springer, 2003;235-9.
75. Vardi MY, Wolper P. An automata-theoretic approach to automatic program verification. In: Proceedings of the First Symposium on Logic in Computer Science. New York: IEEE press, 1986;322-31.
76. Monniaux D. The pitfalls of verifying floating-point computations. TOPLAS 2008;30(3):1-41.
77. Defour D. Fonctions élémentaires: algorithmes et implémentations efficaes pour l'arrondi correct en double précision. PhD diss, É cole Normale Supérieure de Lyon, Lyon, France, 2003.
78. Björndalen J, Anshus O. Trusting floating point benchmarks-are your benchmarks really data independent?Applied Parallel Computing. State of the Art in Scientific Computing. Berlin/Heidelberg, New York: Springer, 2010;178-88.
79. Berger SA, Krompaß D, Stamatakis A. Performance, accuracy, and web-server for evolutionary placement of short sequence reads under maximum-likelihood. Technical Report. http://arxiv.org/abs/0911.2852v1 (November 29, 2010, date last accessed).
80. Miller G. A Scientist's nightmare: Software problem leads to five retractions. Science 2006;384(5807):1856-7.
81. Pomeranz Krummel DA, Altman S. Verification of phylogenetic predictions in vivo and the importance of the tetraloop motif in a catalytic RNA. Proc Natl Acad Sci USA 1999; 96:11200-5.
82. Dunn CW, Hejnol A, Matus DQ, etal. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc RSoc B 2009;276(1677):4261-70.
83. Philippe H, Derelle R, Lopez P, et al. Phylogenomics revives traditional views on deep animal relationships. Curr Biol 2009;19(8):706-12.
84. Schierwater B, Eitel M, Jakob W, et al. Concatenated analysis sheds light on early metazoan evolution and fuels a modern 'urmetazoon' hypothesis. PloS Biol 2009;7(1):e20.
85. Pick KS, Philippe H, Schreiber F, et al. Improved phylogenomic taxon sampling noticeably affects non-bilaterian relationships. Mol Biol Evol 2010;27(9):1983-87.
86. Holder MT, Lewis PO, Swofford DL, et al. Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics. Syst Biol 2005;54(6):961-5.