Polynomial supertree methods revisited

Advances in Bioinformatics

Volumn 2011, Issue , 2011, Pages

  Brinkmeyer, Malte ^a   Griebel, Thasso ^a   Böcker, Sebastian ^a  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84855571832     PISSN: 16878027     EISSN: 16878035     Source Type: Journal    
DOI: 10.1155/2011/524182     Document Type: Article

References (55)

1. Bininda-Emonds O. R. P., The evolution of supertrees Trends in Ecology and Evolution 2004 19 6 315 322 (Pubitemid 38729833)
2. Gordon A. D., Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves Journal of Classification 1986 3 2 335 348
3. Bininda-Emonds O. R. P., Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life 2004 4 Dordrecht, The Netherlands Kluwer Academic Publishers Computational Biology Book Series
4. de Queiroz A., Gatesy J., The supermatrix approach to systematics Trends in Ecology and Evolution 2007 22 1 34 41 (Pubitemid 44959174)
5. Bininda-Emonds O. R. P., Cardillo M., Jones K. E., MacPhee R. D. E., Beck R. M. D., Grenyer R., Price S. A., Vos R. A., Gittleman J. L., Purvis A., The delayed rise of present-day mammals Nature 2007 446 7135 507 512 (Pubitemid 46514725)
6. Roch S., A short proof that phylogenetic tree reconstruction by maximum likelihood is hard IEEE/ACM Transactions on Computational Biology and Bioinformatics 2006 3 1 92 94 (Pubitemid 43269830)
7. Foulds L. R., Graham R. L., The steiner problem in phylogeny is NP-complete Advances in Applied Mathematics 1982 3 1 43 49
8. Stamatakis A., Ludwig T., Meier H., Parallel inference of a 10.000-taxon phylogeny with maximum likelihood 3149 Proceedings of International Euro-Par Conference (Euro-Par '04) 2004 Springer 997 1004 Lecture Notes in Computer Science
9. Bininda-Emonds O. R. P., Supertree construction in the genomic age Methods in Enzymology 2005 395 745 757 (Pubitemid 40754395)
10. Baum B. R., Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees Taxon 1992 41 1 3 10
11. Ragan M. A., Matrix representation in reconstructing phylogenetic relationships among the eukaryotes BioSystems 1992 28 13 47 55 (Pubitemid 23043822)
12. Chen D., Eulenstein O., Fernndez-Baca D., Sanderson M., Minimum-flip supertrees: complexity and algorithms IEEE/ACM Transactions on Computational Biology and Bioinformatics 2006 3 2 165 173
13. Rodrigo A., A comment on baum method for combining phylogenetic trees Taxon 1993 42 631 636
14. Ross H., Rodrigo A., Bininda-Emonds O. R., An assessment of matrix representation with compatibility in supertree construction Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life 2004 4 Dordrecht, The Netherlands Kluwer Academic Publishers 35 63 Computational Biology Book Series
15. Page R. D. M., Modified mincut supertrees 2452 Proceedings of Workshop on Algorithms in Bioinformatics (WABI '02) 2002 Springer 537 552 Lecture Notes in Computer Science
16. Aho A. V., Sagiv Y., Szymanski T. G., Ullman J. D., Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions SIAM Journal on Computing 1981 10 3 405 421
17. Semple C., Steel M., A supertree method for rooted trees Discrete Applied Mathematics 2000 105 13 147 158
18. Willson S. J., Constructing rooted supertrees using distances Bulletin of Mathematical Biology 2004 66 6 1755 1783 (Pubitemid 39444491)
19. Cotton J. A., Slater C. S., Wilkinson M., Discriminating supported and unsupported relationships in supertrees using triplets Systematic Biology 2006 55 2 345 350
20. Goloboff P. A., Minority rule supertrees? MRP, compatibility, and minimum flip may display the least frequent groups Cladistics 2005 21 3 282 294 (Pubitemid 41537317)
21. Goloboff P. A., Pol D., Semi-strict supertrees Cladistics 2002 18 5 514 525 (Pubitemid 36374534)
22. Bininda-Emonds O. R. P., Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees Systematic Biology 2003 52 6 839 848 (Pubitemid 38106049)
23. Ranwez V., Berry V., Criscuolo A., Fabre P. H., Guillemot S., Scornavacca C., Douzery E. J., PhySIC: a veto supertree method with desirable properties Systematic Biology 2007 56 5 798 817
24. Scornavacca C., Berry V., Lefort V., Douzery E. J. P., Ranwez V., PhySICIST: cleaning source trees to infer more informative supertrees BMC Bioinformatics 2008 9, article 413
25. Criscuolo A., Berry V., Douzery E. J., Gascuel O., SDM: a fast distance-based approach for (super) tree building in phylogenomics Systematic Biology 2006 55 5 740 755
26. Huson D. H., Nettles S. M., Warnow T. J., Disk-covering, a fast-converging method for phylogenetic tree reconstruction Journal of Computational Biology 1999 6 3-4 369 386
27. Huson D. H., Vawter L., Warnow T. J., Solving large scale phylogenetic problems using DCM2 Proceedings of International Conference on Intelligent Systems for Molecular Biology (ISMB '99) 1999 118 129
28. Roshan U. W., Warnow T., Moret B. M. E., Williams T. L., Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees Proceedings of IEEE Computational Systems Bioinformatics Conference (CSB '04) August 2004 98 109 (Pubitemid 40276243)
29. Bininda-Emonds O. R. P., Sanderson M. J., Assessment of the accuracy of matrix representation with parsimony analysis supertree construction Systematic Biology 2001 50 4 565 579
30. Buerki S., Forest F., Salamin N., Alvarez N., Comparative performance of supertree algorithms in large data sets using the soapberry family (sapindaceae) as a case study Systematic Biology 2011 60 1 32 44
31. Eulenstein O., Chen D., Burleih J. G., Fernndez-Baca D., Sanderson M. J., Performance of flip supertree construction with a heuristic algorithm Systematic Biology 2004 53 2 299 308 (Pubitemid 38611184)
32. Levasseur C., Lapointe F.-J., Total evidence, average consensus and matrix representation with parsimony: what a difference distances make Evolutionary Bioinformatics 2006 2 249 253
33. Swenson M. S., Barbanon F., Warnow T., Linder C. R., A simulation study comparing supertree and combined analysis methods using SMIDGen Algorithms for Molecular Biology 2010 5 1, article 8
34. Semple C., Steel M. A., Phylogenetics 2003 Oxford University Press Oxford Lecture Series in Mathematics and Its Applications
35. Thorley J. L., Wilkinson M., Jannowitz M., Lapointe F., McMorris F., Roberts F., A view of supertree methods Bioconsensus 2003 61 The American Mathematical Society
36. Lapointe F. J., Cucumel G., The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa Systematic Biology 1997 46 2 306 311 (Pubitemid 127363920)
37. Lapointe L. C., Phylogenetic supertrees: combining information to reveal the tree of life Everything You always Wanted to Know about the Average Consensus and More 2004 Dordrecht, The Netherlands Kluwer Academic Publishers 87 106
38. Criscuolo A., Gascuel O., Fast NJ-like algorithms to deal with incomplete distance matrices BMC Bioinformatics 2008 9, article 166
39. Baum B. R., Ragan M. A., Bininda-Emonds O. R., The MRP method Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life 2004 4 chapter 1 Dordrecht, The Netherlands Kluwer Academic Publishers 17 34 Computational Biology Book Series
40. Fitch W. M., Toward defining the course of evolution: minimum change for a specific tree topology Systematic Zoology 1971 20 4 406 416
41. Sanderson M. J., r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock Bioinformatics 2003 19 2 301 302 (Pubitemid 36181923)
42. Rambaut A., Grassly N. C., Seq-gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees Computer Applications in the Biosciences 1997 13 3 235 238 (Pubitemid 27249927)
43. Yang Z., Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods Journal of Molecular Evolution 1994 39 3 306 314 (Pubitemid 24283346)
44. Higdon J. W., Bininda-Emonds O. R. P., Beck R. M. D., Ferguson S. H., Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset BMC Evolutionary Biology 2007 7 1, article 216
45. Stamatakis A., RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Bioinformatics 2006 22 21 2688 2690 (Pubitemid 44642609)
46. Swafford D., Paup: phylogenetic analysis using parsimony (and other methods) 2002. Version 4
47. Griebel T., Brinkmeyer M., Bcker S., EPoS: a modular software framework for phylogenetic analysis Bioinformatics 2008 24 20 2399 2400
48. Robinson D. F., Foulds L. R., Comparison of phylogenetic trees Mathematical Biosciences 1981 53 1-2 131 147 (Pubitemid 11129084)
49. Day W., Analysis of quartet dissimilarity measures between undirected phylogenetic trees Systematic Biology 1986 35 325 333
50. Gordon A. D., Tomassine R., On the assessment and comparison of classifications Analyse de Donnees et Informatique 1980 Le Chesnay, France INRIA 149 160
51. Colless D. H., Congruence between morphometric and allozyme data for menidia species: a reappraisal Systematic Zoology 1980 29 3 288 299
52. Colless D. H., Predictivity and stability in classifications: some comments on recent studies Systematic Zoology 1981 30 3 325 331
53. Bininda-Emonds O. R. P., The future of supertrees: bridging the gap with supermatrices 3 Proceedings of Willi-Hennig-Symposium 2009 2010 99 106 Supplement of Palaeodiversity
54. Kupczok A., Schmidt H. A., von Haeseler A., Accuracy of phylogeny reconstruction methods combining overlapping gene data sets Algorithms for Molecular Biology 2010 5 37
55. Swenson M. S., Suri R., Linder C. R., Warnow T., An experimental study of Quartets MaxCut and other supertree methods Algorithms for Molecular Biology 2011 6 1, article 7