AxPcoords & parallel AxParafit: Statistical co-phylogenetic analyses on thousands of taxa

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Stamatakis, Alexandros ^a,b   Auch, Alexander F ^b   Meier Kolthoff, Jan ^b   Göker, Markus ^b  

^a EPFL   (Switzerland)

^b UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION MATRIX; DATA SET SIZE; EMPIRICAL STUDIES; LARGE DATASETS; MEMORY FOOTPRINT; PARALLEL ANALYSIS; PARALLEL IMPLEMENTATIONS; PERFORMANCE BENEFITS;

C (PROGRAMMING LANGUAGE); OPTIMIZATION; PROGRAM PROCESSORS; TOOLS;

PARALLEL PROCESSING SYSTEMS;

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; FUNGAL GENETICS; GENETIC ALGORITHM; HOST PARASITE INTERACTION; NONHUMAN; PHYLOGENY; PLANT GENETICS; STATISTICAL ANALYSIS; TAXONOMY; ALGORITHM; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER SIMULATION; DNA SEQUENCE; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; STATISTICAL MODEL;

FUNGI;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; EVOLUTION, MOLECULAR; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 38049165771     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-405     Document Type: Article

References (48)

1. Page RDM Tangled Trees. Phylogeny, Cospeciation and Coevolution The University of Chicago Press 2002. chap. Introduction
2. Goloboff P Analyzing large data sets in reasonable times: Solution for composite optima Cladistics 1999, 15:415-428. 10.1111/ j.1096-0031.1999.tb00278.x
3. Ronquist F Huelsenbeck J MrBayes 3: Bayesian phylogenetic inference under mixed models Bioinformatics 2003, 19(12):1572-1574. 10.1093/ bioinformatics/btg180 12912839
4. Zwickl D Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion PhD thesis University of Texas at Austin 2006.
5. Stamatakis A RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Bioinformatics 2006, 22(21):2688-2690. 10.1093/bioinformatics/btl446 16928733
6. Grimm GW Renner SS Stamatakis A Hemleben V A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analyses of 606 Sequences Evolutionary Bioinformatics Online 2006, 2:279-294.
7. McMahon MM Sanderson MJ Phylogenetic Supermatrix Analysis of GenBank Sequences from 2228 Papilionoid Legumes Systematic Biology 2006, 55(5):818-836. 10.1080/10635150600999150 17060202
8. Bininda-Emonds ORP Cardillo M Jones KE MacPhee RDE Beck RMD Grenyer R Price SA Vos RA Gittleman JL Purvis A The delayed rise of present-day mammals Nature 2007, 446:507-512. 10.1038/nature05634 17392779
9. DeSantis TZ Hugenholtz P Larsen N Rojas M Brodie EL Keller K Huber T Dalevi D Hu P Andersen GL Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB Applied Environmental Microbiology 2006, 72(7):5069-5072. 10.1128/AEM.03006-05
10. Soltis DE Gitzendanner MA Soltis PS A 567-taxon data set for angiosperms: The challenges posed by bayesian analyses of large data sets International Journal of Plant Sciences 2007, 168(2):137-157. 10.1086/509788
11. Robertson CE Harris JK Spear JR Pace NR Phylogenetic diversity and ecology of environmental Archaea Current Opinion in Microbiology 2005, 8:638-642. 16236543
12. Ley RE Harris JK Wilcox J Spear JR Miller SR Bebout BM Maresca JA Bryant DA Sogin ML Pace NR Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat Applied Environmental Microbiology 2006, 72(5):3685-3695. 10.1128/AEM.72.5.3685-3695.2006
13. Stevens J Computational aspects of host-parasite phylogenies Briefings in Bioinformatics 2004, 5(4):339-349. 10.1093/bib/5.4.339 15606970
14. Meier-Kolthoff JP Auch AF Huson DH Göker M COPYCAT: Co-phylogenetic analysis tool Bioinformatics 2007, 23(7):898-900. 10.1093/bioinformatics/ btm027 17267434
15. Legendre P Desdevises Y Bazin E A statistical test for host-parasite coevolution Systematic Biology 2002, 51(2):217-234. 10.1080/ 10635150252899734 12028729
16. Ricklefs R Fallon S Birmingham E Evolutionary relationships, cospeciation, and host switching in avian malaria parasites Systematic Biology 2004, 53:111-119. 10.1080/10635150490264987 14965906
17. Hansen H Bachmann L Bakke T Mitochondrial DNA variation of Gyrodactylus spp. (Monogenea, Gyrodactylidae) populations infecting Atlantic salmon, grayling, and rainbow trout in Norway and Sweden International Journal of Parasitology 2003, 33(13):1471-1478. 10.1016/S0020-7519(03)00200-5 14572510
18. Meinilä M Kuusela J Zietara MS Lumme J Initial steps of speciation by geographic isolation and host switch in salmonid pathogen Gyrodactylus salaris (Monogenea: Gyrodactylidae) International Journal of Parasitology 2004, 34(4):515-526. 10.1016/j.ijpara.2003.12.002 15013741
19. Huyse T Audenart V Volckaert FA Speciation and host-parasite relationships in the parasite genus Gyrodactylus (Monogenea, Platyhelminthes) infecting gobies of the genus Pomatoschistus (Gobiidae, Teleostei) International Journal Parasitology 2003, 33(14):1679-1689. 10.1016/S0020-7519(03)00253-4
20. Legendre P Anderson MJ Program DistPCoA Département de sciences biologiques, Université de Montréal 1998.
21. Basic Linear Algebra Package http://www.netlib.org/blas
22. Linear Algebra PACKage http://www.netlib.org/lapack
23. AMD Core Math Library http://www.amd.com/acml
24. GNU scientific library http://www.gnu.org/software/gsl
25. Bai Z Fahey M Golub G Some large-scale matrix computation problems Journal of Computational and Applied Mathematics 1996, 74:71-89. 10.1016/ 0377-0427(96)00018-0
26. Griffith DA Eigenfunction properties and approximations of selected incidence matrices employed in spatial analyses Linear Algebra and its Applications 2000, 321:95-112. 10.1016/S0024-3795(00)00031-8
27. Bollhöfer M Notay Y JADAMILU: A code for computing selected eigenvalues of large sparse symmetric matrices Tech rep Université Libre de Bruxelles, Brussels 2006. http://homepages.ulb.ac.be/~jadamilu/
28. Press WH Teukolsky SA Vetterling WT Flannery BP Numerical Recipes in C Cambridge University Press 1992.
29. EMBL database http://www.ebi.ac.uk/embl
30. Bauer R Begerow D Oberwinkler F Piepenbring M Berbee M Ustilaginomycetes The Mycota 2001, 7(Part B):57-83.
31. Vanky K European Smut Fungi G. Fischer 1994.
32. Thomas P Menzies J Cereal smuts in Manitoba and Saskatchewan, 1989-95 Canadian Journal of Plant Pathology 1997, 19(2):161-165.
33. Begerow D Bauer R Oberwinkler F The Exobasidiales: An evolutionary hypothesis Mycological Progress 2002, 1(2):187-199. 10.1007/ s11557-006-0018-7
34. Jackson A A Reconciliation Analysis of Host Switching in Plant-Fungal Symbioses Evolution 2004, 58(9):1909-1923. 15521451
35. Vanky K European Smut Fungi (Ustilaginomycetes p.p. and Microbotryales) according to recent nomenclature Mycologia Balcanica 2005, 2:169-178.
36. Bauer R Vanky K Begerow D Oberwinkler F Ustilaginomycetes on Selaginella Mycologia 1999, 91(3):475-484. 10.2307/3761348
37. Bauer R Begerow D Nagler A Oberwinkler F The Georgefischeriales: A Phylogenetic Hypothesis Mycological Research 2001, 105(04):416-424. 10.1017/S0953756201003690
38. Bauer R Lutz M Oberwinkler F Gjaerumia, a new genus in the Georgefischeriales (Ustilaginomycetes) Mycological Research 2005, 109(11):1250-1258. 10.1017/S0953756205003783 16279418
39. Begerow D Bauer R Oberwinkler F Muribasidiospora: Microstromatales or Exobasidiales? Mycological Research 2001, 105(07):798-810. 10.1017/ S0953756201004208
40. de Beer Z Begerow D Bauer R Pegg G Crous P Wingfield M Phylogeny of the Quambalariaceae fam. nov., including important Eucalyptus pathogens in South Africa and Australia Studies in Mycology 2006, 55:289-298.
41. Hendrichs M Bauer R Oberwinkler F The Cryptobasidiaceae of tropical Central and South America Sydowia 2003, 55:33-64.
42. Nannfeldt J Exobasidium, a taxonomic reassessment applied to the European species Symbolae Botanicae Upsaliensis 1981, 23:1-72.
43. Piepenbring M Smut fungi: (Ustilaginomycetes p.p. and Microbotryales, Basidiomycota) Flora Neotropica Monograph 2003, 86:1-291.
44. Scholz H Scholz I Die Brandpilze Deutschlands (Ustilaginales) Englera 1988, 8:1-691. 10.2307/3776736
45. Vanky K McKenzie E Smut fungi of New Zealand Fungal Diversity Press, Centre for Research in Fungal Diversity, Dept. of Ecology & Biodiversity, University of Hong Kong Hong Kong 2002.
46. GenBank http://www.ncbi.nlm.nih.gov
47. Palese R Moser D Synonymie-Index der Schweizer Flora und der angrenzenden Gebiete Tech rep Zentrum des Datenverbundnetzes der Schweizer Flora 1997.
48. PLOS retraction http://compbiol.plosjournals.org/perlserv/?request= get-document&doi=10.1371/journal.pcbi.0030158