Parallelizing SuperFine

Proceedings of the ACM Symposium on Applied Computing

Volumn , Issue , 2012, Pages 1361-1367

  Neves, Diogo Telmo ^a   Warnow, Tandy ^b   Sobral, João Luís ^c   Pingali, Keshav ^b  

^a POLYTECHNIC INSTITUTE OF PORTO   (Portugal)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c UNIVERSITY OF MINHO   (Portugal)

Author keywords

irregular applications; parallelization; phylogeny estimation; polytomy; shared memory; supertree

Indexed keywords

DATA SETS; ESTIMATION METHODS; EVOLUTIONARY TREE; GRAND CHALLENGE; MODERN BIOLOGY; PARALLEL IMPLEMENTATIONS; PARALLELIZATIONS; PARALLELIZING; POLYTOMY; RESEARCH GROUPS; SHARED MEMORIES; SUBTREES; SUPERTREE; TREE OF LIFE;

BINARY TREES; BIOLOGY; COMPUTATIONAL COMPLEXITY; ESTIMATION;

FORESTRY;

BIOLOGY; COMPUTATION; FORESTRY;

EID: 84863572075     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2245276.2231992     Document Type: Conference Paper

References (33)

1. M. Bansal, J. G. Burleigh, O. Eulenstein, and D. Fernández-Baca. Robinson-Foulds supertrees. Algorithms for Molecular Biology, 5:18, 2009.
2. B. R. Baum. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon, 41:3-10, 1992.
3. B. R. Baum and M. A. Ragan. The MRP method. In O. R. P. Bininda-Emonds, editor, Phylogenetic Supertrees: combining information to reveal The Tree Of Life, pages 17-34. Kluwer Academic, Dordrecht, the Netherlands, 2004.
4. R. M. D. Beck, O. R. P. Bininda-Emonds, M. Cardillo, F. G. R. Liu, and A. Purvis. A higher-level MRP supertree of placental mammals. BMC Evol. Biol., 6:93, 2006.
5. O. R. P. Bininda-Emonds. Phylogenetic Supertrees: combining information to reveal The Tree Of Life. Computational Biology. Kluwer Academic, Dordrecht, the Netherlands, 2004.
6. J. G. Burleigh, O. Eulenstein, D. Fernández-Baca, and M. J. Sanderson. MRF supertrees. In O. R. P. Bininda-Emonds, editor, Phylogenetic Supertrees: combining information to reveal The Tree Of Life, pages 65-86. Kluwer Academic, Dordrecht, the Netherlands, 2004.
7. M. Cardillo, O. R. P. Bininda-Emonds, E. Boakes, and A. Purvis. A species-level phylogenetic supertree of marsupials. J. Zool., 264:11-31, 2004. (Pubitemid 39246912)
8. D. Chen, O. Eulenstein, D. Ferńandez-Baca, and M. J. Sanderson. Minimum-flip supertrees: Complexity and algorithms. IEEE/ACM Trans. Comp. Biol. Bioinform., 3:165-173, 2006.
9. J. A. Cotton and M. Wilkinson. Majority-rule supertrees. Syst. Biol., 56(3):445-452, 2007.
10. L. R. Foulds and R. L. Graham. The Steiner problem in phylogeny is NP-complete. Advances in Applied Mathematics, 3:43-49, 1982.
11. D. H. Huson, S. M. Nettles, and T. J. Warnow. Disk-covering, a fast-converging method for phylogenetic tree reconstruction. JOURNAL OF COMPUTATIONAL BIOLOGY, 6(3):369-386, 1999.
12. T. Jiang, P. Kearney, and M. Li. A polynomial-time approximation scheme for inferring evolutionary trees from quartet topologies and its applications. SIAM J. Comput., 30(6):1924-1961, 2001.
13. M. Kennedy and R. Page. Seabird supertrees: combining partial estimates of procellariiform phylogeny. The Auk, 119:88-108, 2002. (Pubitemid 34231482)
14. K. Liu, C. Linder, R. Suri, and T. Warnow. Multiple sequence alignment: a major challenge to large-scale phylogenetics. PLoS Currents: Tree of Life, 2010.
15. K. Liu, T. J. Warnow, M. T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C. R. Linder. SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst Biol, 2011. In press.
16. M. McMahon and M. Sanderson. Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Syst. Biol., 55(5):818-836, 2006.
17. K. C. Nixon. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics, 15(4):407-414, 1999.
18. M. A. Ragan. Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol., 1:53-58, 1992.
19. V. Ranwez, V. Berry, A. Criscuolo, P. Fabre, S. Guillemot, C. Scornavacca, and E. Douzery. PhySIC: a veto supertree method with desirable properties. Syst. Biol., 56(5):798-817, 2007.
20. V. Ranwez, A. Criscuolo, and E. J. Douzery. SuperTriplets: a triplet-based supertree approach to phylogenomics. Bioinformatics, 26(12):i115-i123, 2010.
21. S. Roch. A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. IEEE Trans. Comput. Biol. and Bioinformatics, 3(1):92-94, 2006. (Pubitemid 43269830)
22. F. Ronquist and J. Huelsenbeck. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19:1572-1574, 2003. (Pubitemid 37038874)
23. U. Roshan, B. M. E. Moret, T. L. Williams, and T. Warnow. Performance of supertree methods on various data-set decompositions. In O. R. P. Bininda-Emonds, editor, Phylogenetic Supertrees: combining information to reveal The Tree Of Life, pages 301-328. Kluwer Academic, Dordrecht, the Netherlands, 2004.
24. A. Stamatakis. RAxML-NI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22:2688-2690, 2006. (Pubitemid 44642609)
25. M. Steel. The complexity of reconstructing trees from qualitative characters and subtrees. J Classification, 9(1):91-116, 1992.
26. M. Steel and A. Rodrigo. Maximum likelihood supertrees. Syst. Biol., 57(2):243-250, 2008. (Pubitemid 351502944)
27. M. S. Swenson, F. Barbançon, C. Linder, and T. Warnow. A simulation study comparing supertree and combined analysis methods using SMIDGen. In Proceedings of the 2009 Workshop on Algorithms in Bioinformatics (WABI), pages 333-344, 2009.
28. M. S. Swenson, F. Barbançon, C. Linder, and T. Warnow. A simulation study comparing supertree and combined analysis methods using SMIDGen. Algorithms for Molecular Biology, 5(8), 2010.
29. M. S. Swenson, R. Suri, C. Linder, and T. Warnow. An experimental study of Quartets MaxCut and other supertree methods. In Proceedings of the 2010 Workshop on Algorithms in Bioinformatics (WABI), 2010.
30. M. S. Swenson, R. Suri, C. Linder, and T. Warnow. An experimental study of Quartets MaxCut and other supertree methods. Algorithms for Molecular Biology, 2010.
31. M. S. Swenson, R. Suri, C. R. Linder, and T. Warnow. SuperFine: Fast and accurate supertree estimation. Syst Biol, 2011. In press.
32. D. L. Swofford. PAUP*. phylogenetic analysis using parsimony (*and other methods). version 4. Sinauer Associates, 2003.
33. M. Wojciechowski, M. Sanderson, K. Steele, and A. Liston. Molecular phylogeny of the "temperate herbaceous tribes" of papilionoid legumes: a supertree approach. Adv. Legume Syst., 9:277-298, 2000.