Treelength optimization for phylogeny estimation

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Liu, Kevin ^a   Warnow, Tandy ^a  

^a University of Texas at Austin   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTROLLED STUDY; DATA ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; MAXIMUM LIKELIHOOD METHOD; PARSIMONY ANALYSIS; PHYLOGENY; PROCESS OPTIMIZATION; TREELENGTH ANALYSIS; DNA SEQUENCE; METHODOLOGY; SEQUENCE ALIGNMENT;

COLEOPTERA;

PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84858612979     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0033104     Document Type: Article

References (59)

1. Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T, (2009) Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324: 1561-1564.
2. Liu K, Linder CR, Warnow T, (2010) Multiple sequence alignment: a major challenge to large-scale phylogenetics. PLoS Currents: Tree of Life 2: RRN1198.
3. Redelings B, Suchard M, (2005) Joint Bayesian estimation of alignment and phylogeny. Syst Biol 54: 401-418.
4. Fleissner R, Metzler D, von Haeseler A, (2005) Simultaneous statistical multiple alignment and phylogeny reconstruction. Syst Biol 54: 548-561.
5. Novák A, Miklós I, Lyngso R, Hein J, (2008) StatAlign: an extendable software package for joint bayesian estimation of alignments and evolutionary trees. Bioinf 24: 2403-2404.
6. Lunter GA, Miklos I, Song YS, Hein J, (2003) An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees. J Comp Biol 10: 869-89.
7. Lunter G, Miklós I, Drummond A, Jensen JL, Hein J, (2005) Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinf 6: 83.
8. Lunter G, Miklós I, Drummond A, Jensen JL, Hein J, (2003) Bayesian phylogenetic inference under a statistical indel model. In: Benson G, Page R, editors. Lecture Notes in Bioinformatics: Third International Workshop, WABI 2003, LNBI Berlin Springer-Verlag, volume 2812 pp. 228-244.
9. Lunter G, Drummond A, Miklós I, Hein J, (2005) Statistical alignment: Recent progress, new applications, and challenges. In: Nielsen R, editors. Statistical Methods in Molecular Evolution (Statistics for Biology and Health) Berlin Springer pp. 375-406.
10. Metzler D, (2003) Statistical alignment based on fragment insertion and deletion models. Bioinf 19: 490-499.
11. Miklós I, (2003) Algorithm for statistical alignment of sequences derived from a Poisson sequence length distribution. Disc Appl Math 127: 79-84.
12. Miklós I, Lunter GA, Holmes I, (2004) A "long indel model" for evolutionary sequence alignment. Mol Biol Evol 21: 529-540.
13. Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T, (2009) Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324: 1561-1564.
14. Liu K, Warnow T, Holder M, Nelesen S, Yu J, et al. (2011) SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst Biol 61: 90-106.
15. Yu J, Holder MT, Sukumaran J, Mirarab S, SATé version 2.1.0. Website. Available athttp://phylo.bio.ku.edu/software/sate/sate.html.
16. Edgar RC, Sjölander K, (2003) SATCHMO: Sequence alignment and tree construction using hidden Markov models. Bioinf 19: 1404-1411.
17. Hagopian R, Davidson J, Datta R, Jarvis G, Sjölander K, (2010) SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction. Nucl Acids Res 38 (Web Server Issue): W29-W34.
18. Varón A, Vinh L, Wheeler W, (2010) POY version 4: phylogenetic analysis using dynamic homologies. Cladistics 26.
19. Varón A, Vinh L, Bomash I, Wheeler W, (2007) POY Software. Documentation by A. Varon, L.S. Vinh, I. Bomash, W. Wheeler, K. Pickett, I. Temkin, J. Faivovich, T. Grant, and W.L. Smith. Available for download athttp://research.amnh.org/scicomp/projects/poy.php.
20. Foulds LR, Graham RL, (1982) The Steiner problem in phylogeny is NP-complete. Adv Appl Math 3: 43-49.
21. Sankoff D, Cedergren R, (1983) Simultaneous comparison of three or more sequences related by a tree. Time Warps, String Edits, and Macromolecules: the Theory and Practice of Sequence Comparison Addison-Wesley pp. 253-264 Chapter 9.
22. Giribet G, (2001) Exploring the behavior of POY, a program for direct optimization of molecular data. Cladistics 17: S60-S70.
23. Kjer K, Gillespie J, Ober K, (2007) Opinions on multiple sequence alignment, and an empirical comparison on repeatability and accuracy between POY and structural alignment. Syst Biol 56: 133-146.
24. Ogden TH, Rosenberg M, (2007) Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW+PAUP*. Syst Biol 56: 182-193.
25. Morrison DA, (2009) Why would phylogeneticists ignore computerized sequence alignment? Syst Biol 58: 150-158.
26. Blair C, Murphy RW, (2011) Recent trends in molecular phylogenetic analysis: Where to next? J Hered 102: 130-138.
27. Yoshizawa K, (2010) Direct optimization overly optimizes data. Syst Ent 35: 199-206.
28. Wheeler W, Giribet G, (2009) Phylogenetic hypotheses and the utility of multiple sequence alignment. In: Rosenberg M, editors. Sequence alignment: methods, models, concepts and strategies University of California Press pp. 95-104.
29. Lehtonen S, (2008) Phylogeny estimation and alignment via POY versus Clustal+PAUP*: A response to Ogden and Rosenberg. Syst Biol 57: 653-657.
30. Thompson J, Higgins D, Gibson T, (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucl Acids Res 22: 4673-4680.
31. Liu K, Nelesen S, Raghavan S, Linder C, Warnow T, (2009) Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy. IEEE Trans Comp Biol Bioinf 6: 7-21.
32. Nelesen S, Liu K, Zhao D, Linder CR, Warnow T, (2008) The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses. Pacific Symposium on Biocomputing. volume 13 pp. 15-24.
33. Wang L, Jiang T, (1994) On the complexity of multiple sequence alignment. J Comp Biol 1: 337-348.
34. Stamatakis A, (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinf 22: 2688-2690.
35. Swofford D, (1996) PAUP*: Phylogenetic analysis using parsimony (and other methods), version 4.0 Sunderland, Mass. Sinauer Assoc.
36. Katoh K, Kuma K, Miyata T, Toh H, (2005) Improvement in the acccuracy of multiple sequence alignment mafft. Genome Inf 16: 22-33.
37. Wheeler T, Kececioglu J, (2007) Multiple alignment by aligning alignments. Bioinf 23: i559-i568.
38. Loytynoja A, Goldman N, (2005) An algorithm for progressive multiple alignment of sequences with insertions. Proc Nat Acad Sci 102: 10557-10562.
39. Huelsenbeck J, Ronquist R, (2001) MrBayes: Bayesian inference of phylogeny. Bioinf 17: 754-755.
40. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
41. Zwickl D, (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. thesis, The University of Texas at Austin.
42. Price M, Dehal P, Arkin A, (2009) FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641-1650.
43. Price M, Dehal P, Arkin A, (2010) FastTree 2- approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490.
44. Helaers R, Milinkovitch MC, (2010) Metapiga v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics. BMC Bioinf 11: 379.
45. Whelan S, Goldman N, (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691-699.
46. Stoye J, Evers D, Meyer F, (1998) Rose: generating sequence families. Bioinf 14: 157-163.
47. Cannone J, Subramanian S, Schnare M, Collett J, D'Souza L, et al. (2002) The Comparative RNA Web (CRW) Site: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron and Other RNAs. BMC Bioinf 3.
48. Katoh K, Kuma K, Toh H, Miyata T, (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucl Acids Res 33: 511-518.
49. Katoh K, Toh H, (2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinf 23: 372-374.
50. Katoh K, Toh H, (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinf 9: 286-298.
51. Do C, Mahabhashyam M, Brudno M, Batzoglou S, (2005) PROBCONS: Probabilistic consistency-based multiple sequence alignment. Genome Res 15: 330-340.
52. Stamatakis A, (2006) Phylogenetic models of rate heterogeneity: A high performance computing perspective. Proceedings of IPDPS2006 HICOMB Workshop, Rhodos, Greece.
53. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinf 22: 2688-2690.
54. Swofford DL, (2003) PAUP*. phylogenetic analysis using parsimony (*and other methods). version 4. Sinauer Associates.
55. Ganapathy G, Ramachandran V, Warnow T, (2003) Better hill-climbing seaches for parsimony. Proceedings of the Third International Workshop on Algorithms in Bioinformatics (WABI) pp. 245-258.
56. Rannala B, Huelsenbeck J, Yang Z, Nielsen R, (1998) Taxon sampling and the accuracy of large phylogenies. Syst Biol 47: 702-710.
57. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Stat Soc Series B (Method) 57: 289-300.
58. Litzkow M, (1987) Remote Unix- turning idle workstations into cycle servers. Usenix Summer Conference pp. 381-384.
59. Liu K, (2011) Fast and Accurate Estimation of Large-Scale Phylogenetic Alignments and Trees. Ph.D. thesis, The University of Texas at Austin.