SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Kostka, Martin ^a,b   Uzlikova, Magdalena ^a   Cepicka, Ivan ^a   Flegr, Jaroslav ^a  

^a CHARLES UNIVERSITY   (Czech Republic)

^b UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

DATA INPUT; ITS APPLICATIONS; PHYLOGENETIC ANALYSIS; SIGNAL/NOISE RATIO; SUBSTITUTION RATES; USER FRIENDLY PROGRAM; USER-FRIENDLY TOOL; WHOLE PROCESS;

BIOLOGY;

APPLICATION PROGRAMS;

ARTICLE; ARTIFACT REDUCTION; AUTOANALYSIS; BLASTOCYSTIS; COMPUTER PROGRAM; CONTROLLED STUDY; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIGNAL NOISE RATIO; ANIMAL; BIOLOGY; COMPUTER INTERFACE; GENETICS; METHODOLOGY; PHYLOGENY; TIME;

BLASTOCYSTIS;

PROTOZOAL DNA;

ANIMALS; BLASTOCYSTIS; COMPUTATIONAL BIOLOGY; DNA, PROTOZOAN; PHYLOGENY; SEQUENCE ALIGNMENT; TIME FACTORS; USER-COMPUTER INTERFACE;

EID: 51249125088     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-341     Document Type: Article

References (19)

1. Felsenstein J Cases in which parsimony or compatibility methods will be positively misleading Syst Zool 1978, 27:401-410. 10.2307/2412923
2. Brinkmann H Giesen van der M Zhou Y de Raucourt GP Philippe H An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics Syst Biol 2005, 54:743-757. 10.1080/ 10635150500234609 16243762
3. Gribaldo S Philippe H Pitfalls in tree reconstruction and the phylogeny of eukaryotes Organelles, genomes and Eukaryote phylogeny CRC Press, Boca Raton/London/New York/Washington, D.C Hirt RP, Horner DS 2004:133-152.
4. Bergsten J A review of long-branch attraction Cladistics 2005, 21:163-193. 10.1111/j.1096-0031.2005.00059.x
5. Inagaki Y Susko E Fast NM Roger AJ Covarion Shifts Cause a Long-Branch Attraction Artifact That Unites Microsporidia and Archaebacteria in EF-1a Phylogenies Mol Biol Evol 2004, 21:1340-1349. 10.1093/molbev/ msh130 15034136
6. Brinkmann H Philippe H Archaea Sister Group of Bacteria? Indications from Tree Reconstruction Artifacts in Ancient Phylogenies Mol Biol Evol 1999, 16:817-825. 10368959
7. Zhu G Keithly JS Philippe H What is the phylogenetic position of Cryptosporidium? IJSEM 2000, 50:1673-1681. 10939675
8. Brochier C Phillipe H Phylogeny: A non-hyperthermophilic ancestor for bacteria Nature 2002, 417:224. 10.1038/417244a
9. Hampl V Cepicka I Flegr J Tachezy J Kulda J Critical analysis of the topology and rooting of the parabasalian 16S rRNA tree Mol Phyl Evol 2004, 32:711-723. 10.1016/j.ympev.2004.03.005 15288049
10. Hampl V Vrlik M Cepicka I Pecka Z Kulda J Tachezy J Affiliation of Cochlosoma to trichomonads confirmed by phylogenetic analysis of the small-subunit rRNA gene and a new family concept of the order Trichomonadida IJSEM 2006, 56:305-312. 16403903
11. Bapteste E Susko E Leigh J Ruiz-Trillo I Bucknam J Doolittle WF Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny Mol Phyl Evol 2008, 25:83-91. 10.1093/molbev/msm229
12. Swofford DL PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4. Sinauer Associates, Sunderland, Massachusetts 2002. 12504223
13. Philippe H MUST, a computer package of management utilities for sequences and trees Nucleic Acids Res 1993, 21:5264-5272. 310646 8255784 10.1093/nar/21.22.5264
14. Schmidt HA Strimmer K Vingron M von Haeseler A TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing Bioinformatics 2002, 18:502-504. 10.1093/bioinformatics/18.3.502 11934758
15. Stenzel DJ Boreham PFL Blastocystis hominis revisited Clin Microbiol Rev 1996, 9:563-584. 172910 8894352
16. Tan KSW Singh M Yap EH Recent advances in Blastocystis hominis research: hot spots in terra incognita Int J Parasitol 2002, 32:789-804. 10.1016/ S0020-7519(02)00005-X 12062550
17. Thompson JD Gibson TJ Plewniak F Jeanmougin F Higgins DG The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 1997, 24:4876-4882. 10.1093/nar/25.24.4876
18. Hall TA BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucl Acids Symp Ser 1999, 41:95-98.
19. Posada D Crandall CA MODELTEST: Testing the model of DNA substitution Bioinf 1998, 14:817-818. 10.1093/bioinformatics/14.9.817