SCaFoS: A tool for selection, concatenation and fusion of sequences for phylogenomics

BMC Evolutionary Biology

Volumn 7, Issue SUPPL. 1, 2007, Pages

  Roure, Béatrice ^a   Rodriguez Ezpeleta, Naiara ^a   Philippe, Hervé ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CHIMERA; COMPUTER PROGRAM; CONFERENCE PAPER; CONTROLLED STUDY; FUSION GENE; GENE SEQUENCE; MOLECULAR GENETICS; MONOPHYLY; NONHUMAN; PHYLOGENY; ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGICAL MODEL; DNA SEQUENCE; EVALUATION; GENETIC SELECTION; METHODOLOGY; MOLECULAR EVOLUTION;

CONCATENATED DNA;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; DNA, CONCATENATED; EVOLUTION, MOLECULAR; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 34248188251     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-S1-S2     Document Type: Conference Paper

References (34)

1. Phylogenomics and the reconstruction of the tree of life. F Delsuc H Brinkmann H Philippe, Nat Rev Genet 2005 6 5 361 375 10.1038/nrg1603 15861208
2. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. WR Atchley KR Wollenberg WM Fitch W Terhalle AW Dress, Mol Biol Evol 2000 17 1 164 178 10666716
3. Orthologs, paralogs, and evolutionary genomics (1). EV Koonin, Annu Rev Genet 2005 39 309 338 10.1146/annurev.genet.39.073003.114725 16285863
4. The limits of protein sequence comparison? WR Pearson ML Sierk, Curr Opin Struct Biol 2005 15 3 254 260 10.1016/j.sbi.2005.05.005 15919194
5. The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. GK Philip CJ Creevey JO McInerney, Mol Biol Evol 2005 22 5 1175 1184 10.1093/molbev/msi102 15703245
6. Does adding characters with missing data increase or decrease phylogenetic accuracy? JJ Wiens, Syst Biol 1998 47 4 625 640 10.1080/106351598260635 12066307
7. Phylogenetic supertrees: assembling the trees of live. MJ Sanderson A Purvis C Henze, Tree 1998 13 3 105 109
8. The phylogenetic trunk: maximal inclusion of taxa with missing data in an analysis of the lepospondyli (Vertebrata, Tetrapoda). JS Anderson, Syst Biol 2001 50 2 170 193 10.1080/10635150119889 12116927
9. Phylogenomics. H Philippe F Delsuc H Brinkmann N Lartillot, Annu Rev Ecol Evol Syst 2005 36 541 562 10.1146/annurev.ecolsys.35.112202.130205
10. Obtaining maximal concatenated phylogenetic data sets from large sequence databases. MJ Sanderson AC Driskell RH Ree O Eulenstein S Langley, Mol Biol Evol 2003 20 7 1036 1042 10.1093/molbev/msg115 12777519
11. Identifying optimal incomplete phylogenetic data sets from sequence databases. C Yan JG Burleigh O Eulenstein, Mol Phylogenet Evol 2005 35 3 528 535 10.1016/j.ympev.2005.02.008 15878123
12. Prospects for building the tree of life from large sequence databases. AC Driskell C Ane JG Burleigh MM McMahon BC O'Meara MJ Sanderson, Science 2004 306 5699 1172 1174 10.1126/science.1102036 15539599
13. Missing data, incomplete taxa, and phylogenetic accuracy. JJ Wiens, Syst Biol 2003 52 4 528 538 10.1080/10635150390218330 12857643
14. Phylogenomics of eukaryotes: impact of missing data on large alignments. H Philippe EA Snell E Bapteste P Lopez PW Holland D Casane, Mol Biol Evol 2004 21 9 1740 1752 10.1093/molbev/msh182 15175415
15. Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction? JJ Wiens, Syst Biol 2005 54 5 731 742 10.1080/10635150500234625 16243761
16. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. H Brinkmann M van der Giezen Y Zhou G Poncelin de Raucourt H Philippe, Syst Biol 2005 54 5 743 757 16243762
17. PHYLIP (Phylogene Inference Package). J Felsenstein, Department of Genetics, University of Washington, Seattle 3.6 2001
18. MUST, a computer package of Management Utilities for Sequences and Trees. H Philippe, Nucleic Acids Res 1993 21 22 5264 5272 8255784 10.1093/nar/21.22. 5264
19. NEXUS: an extensible file format for systematic information. DR Maddison DL Swofford WP Maddison, Syst Biol 1997 46 4 590 621 10.2307/2413694 11975335
20. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. HA Schmidt K Strimmer M Vingron A von Haeseler, Bioinformatics 2002 18 3 502 504 10.1093/bioinformatics/18.3.502 11934758
21. Tunicates and not cephalochordates are the closest living relatives of vertebrates. F Delsuc H Brinkmann D Chourrout H Philippe, Nature 2006 439 7079 965 968 10.1038/nature04336 16495997
22. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. H Philippe N Lartillot H Brinkmann, Mol Biol Evol 2005 22 5 1246 1253 10.1093/molbev/msi111 15703236
23. Monophyly of primary photosynthetic eukaryotes: Green plants, red algae, and glaucophytes. N Rodriguez-Ezpeleta H Brinkmann SC Burey B Roure G Burger W Loffelhardt HJ Bohnert H Philippe BF Lang, Current Biology 2005 15 14 1325 1330 10.1016/j.cub.2005.06.040 16051178
24. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 12 1572 1574 10.1093/bioinformatics/ btg180 12912839
25. PAUP*: Phylogenetic Analysis Using Parsimony and other methods. DL Swofford, Sinauer, Sunderland, MA 4b10 2000
26. Cases in which parsimony or compatibility methods will be positively misleading. J Felsenstein, Syst Zool 1978 27 401 410 10.2307/2412923
27. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. G Jobb A von Haeseler K Strimmer, BMC Evol Biol 2004 4 1 18 15222900 10.1186/1471-2148-4-18
28. The rapid generation of mutation data matrices from protein sequences. DT Jones WR Taylor JM Thornton, Comput Appl Biosci 1992 8 3 275 282 1633570
29. Substitutional bias confounds inference of cyanelle origins from sequence data. PJ Lockhart CJ Howe DA Bryant TJ Beanland AW Larkum, Journal of Molecular Evolution 1992 34 2 153 162 10.1007/BF00182392 1556750
30. Coelomata and not ecdysozoa: evidence from genome-wide phylogenetic analysis. YI Wolf IB Rogozin EV Koonin, Genome Res 2004 14 1 29 36 14707168 10.1101/gr.1347404
31. Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. H Dopazo J Santoyo J Dopazo, Bioinformatics 2004 20 Suppl 1 i116 i121 10.1093/bioinformatics/bth902 15262789
32. Genome-scale evidence of the nematode-arthropod clade. H Dopazo J Dopazo, Genome Biology 2005 6 5 R41 15892869 10.1186/gb-2005-6-5-r41
33. Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis. J Castresana, Mol Biol Evol 2000 17 4 540 552 10742046
34. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 5 696 704 10.1080/10635150390235520 14530136