MPI-PHYLIP: Parallelizing computationally intensive phylogenetic analysis routines for the analysis of large protein families

PLoS ONE

Volumn 5, Issue 11, 2010, Pages

  Ropelewski, Alexander J ^a   Nicholas, Hugh B ^a   Mendez, Ricardo R Gonzalez ^b  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b UNIVERSITY OF PUERTO RICO SCHOOL OF MEDICINE   (Puerto Rico)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; CYTOCHROME C OXIDASE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BOOTSTRAPPING; COMPUTER PROGRAM; JACKKNIFE TEST; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MEMORY; PHYLOGENETIC TREE; PHYLOGENY; PROTEIN DATABASE; SEQUENCE ALIGNMENT; ALGORITHM; ANIMAL; BIOLOGY; CLASSIFICATION; GENETICS; HUMAN; METHODOLOGY; REPRODUCIBILITY;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; HUMANS; PHYLOGENY; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 78649757228     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013999     Document Type: Article

References (40)

1. Sheps JA, Ralph S, Zhao Z, Baillie DL, Ling V (2004) The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes. Genome Biol 5: R15.
2. Bridgham JT, Carroll SM, Thornton JW (2006) Evolution of Hormone- Receptor Complexity by Molecular Exploitation. Science 312: 97-101.
3. Durand D, Hoberman R (2006) Diagnosing duplications-can it be done? Trends Genet 22: 156-164.
4. Darling AE, Miklós I, Ragan MA (2008) Dynamics of Genome Rearrangement in Bacterial Populations. PLoS Genet 4: e1000128. doi:10.1371/journal. pgen.1000128.
5. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, et al. (2006) Toward Automatic Reconstruction of a Highly Resolved Tree of Life. Science 311: 1283-1287.
6. Janies DA, Wheeler WC (2002) Theory and practice of parallel direct optimization. EXS 92: 115-123.
7. Douady CJ, Delsuc F, Boucher Y, Doolittle WF, Douzery EJ (2003) Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol Biol Evol 20: 248-254.
8. Durand D, Halldorsson BV, Vernot B (2006) A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction. J Comp Biol 13: 320-335.
9. Kosakovsky-Pond SL, Frost SDW, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
10. Hedges SB (1992) The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies. Mol Biol Evol 9: 366-369.
11. Sanderson MJ, Driskell AC (2003) The challenge of constructing large phylogenetic trees. Trends Plant Sci 8: 373-379.
12. Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6: 361-375.
13. Williams TL, Bader DA, Moret BME, Yan M (2006) High-Performance Phylogeny Reconstruction Under Maximum Parsimony. In Parallel Computing for Bioinformatics and Computational Biology Zomaya AY, ed. John Wiley and Sons. pp 369-394.
14. Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: 564-577.
15. Keane TM, Naughton TJ, Travers SA, McInerney JO, McCormack GP (2005) DPRml: distributed phylogeny reconstruction by maximum likelihood. Bioinformatics 21: 969-974.
16. Keane TM, Naughton TJ, McInerney JO (2007) MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. Nucleic Acids Res 35: W33-W37. doi:10.1093/nar/gkm359.
17. Minh BQ, Vinhle S, von Haeseler A, Schmidt HA (2005) PIQPNNI: parallel reconstruction of large maximum likelihood phylogenies. Bioinformatics 21: 3794-3796.
18. Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F (2004) Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407-415.
19. Li KB (2003) ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 19: 1585-1586.
20. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
21. Stamatakis AP, Ludwig T, Meier H, Wolf MJ (2002) AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method. Proc IEEE Comput Soc Bioinform Conf 1: 21-28.
22. Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456-463.
23. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogeneticanalyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
24. Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm forthe RAxMLWeb servers. Syst Biol 57: 758-771.
25. Kordis D, Turk V (2009) Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes. BMC Evol Biol 9: 266.
26. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
27. Russo CA, Takezaki N, Nei M (1996) Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol Biol Evol 13: 525-536.
28. Felsenstein J (2004) Inferring Phylogenies. Sunderland MA: Sinauer Associates, Inc.
29. Perozich J, Nicholas H, Wang BC, Lindahl R, Hempel J (1999) Relationships within the aldehyde dehydrogenase extended family. Protein Sci 8: 137-146.
30. Hempel J, Perozich J, Wymore T, Nicholas HB (2003) An algorithm for identification and ranking of family-specific residues, applied to the ALDH3 family. Chem Biol Interact 143-144: 23-28.
31. Wymore T, Deerfield DW, 2nd, Field MJ, Hempel J, Nicholas HB, Jr. (2003) Initial catalytic events in class 3 aldehyde dehydrogenase: MM and QM/MM simulations. Chem Biol Interact 143-144: 75-84.
32. Opperdoes FR (2009) Phylogenetic analysis using protein sequences. In The Phylogenetic Handbook Lemey P, Salemi M, Vandamme AM, eds. Cambridge University Press. pp 313-341.
33. Felsenstein J (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
34. Olsen GJ, Matsuda H, Hagstrom R, Overbeek R (1994) FastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 10: 41-48.
35. Felsenstein J, Churchill GA (1996) A Hidden Markov Model Approach to Variation Among Sites in Rate of Evolution. Mol Biol Evol 13: 93-104.
36. Yang S, Doolittle RF, Bourne PE (2005) Phylogeny determined by protein domain content. Proc Nat Acad Sci USA 102: 373-378.
37. Mayr E (2001) What evolution is. New York: Basic Books. 336 p.
38. Sankararaman S, Sjölander K (2008) INTREPID-INformation-theoretic TREe traversal for Protein functional site IDentification. Bioinformatics 24: 2445-2452.
39. Hamacher K (2010) Protein Domain Phylogenies: Information Theory and Evolutionary Dynamics. In: Fred A, Filipe J, Gamboa H, eds. Proceedings of Bioinformatics 2010, 1st International Conference on Bioinformatics. Pp 114-122.
40. Reva B, Antipin Y, Sander C (2007) Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol 8: R232