BACKGROUND: Slow-fast analysis is a simple and effective method to reduce the influence of substitution saturation, one of the causes of phylogenetic noise and long branch attraction (LBA) artifacts. In several steps of increasing stringency, the slow-fast analysis omits the fastest substituting alignment positions from the analysed dataset and thus increases its signal/noise ratio. RESULTS: Our program SlowFaster automates the process of assessing the substitution rate of the alignment positions and the process of producing new alignments by deleting the saturated positions. Its use is very simple. It goes through the whole process in several steps: data input - necessary choices - production of new alignments. CONCLUSION: SlowFaster is a user-friendly tool providing new alignments prepared with slow-fast analysis. These data can be used for further phylogenetic analyses with lower risk of long branch attraction artifacts.

Department of Parasitology Faculty of Science Charles University Vinicna 7 128 44 Prague Czech Republic

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Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 1978;27:401–410. doi: 10.2307/2412923. DOI

Brinkmann H, Giesen M van der, 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. doi: 10.1080/10635150500234609. PubMed DOI

Gribaldo S, Philippe H. Pitfalls in tree reconstruction and the phylogeny of eukaryotes. In: Hirt RP, Horner DS, editor. Organelles, genomes and Eukaryote phylogeny. CRC Press, Boca Raton/London/New York/Washington, D.C; 2004. pp. 133–152.

Bergsten J. A review of long-branch attraction. Cladistics. 2005;21:163–193. doi: 10.1111/j.1096-0031.2005.00059.x. PubMed DOI

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. doi: 10.1093/molbev/msh130. PubMed DOI

Brinkmann H, Philippe H. Archaea Sister Group of Bacteria? Indications from Tree Reconstruction Artifacts in Ancient Phylogenies. Mol Biol Evol. 1999;16:817–825. PubMed

Zhu G, Keithly JS, Philippe H. What is the phylogenetic position of Cryptosporidium? IJSEM. 2000;50:1673–1681. PubMed

Brochier C, Phillipe H. Phylogeny: a non-hyperthermophilic ancestor for bacteria. Nature. 2002;417:224. doi: 10.1038/417244a. PubMed DOI

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. doi: 10.1016/j.ympev.2004.03.005. PubMed DOI

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. PubMed

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. doi: 10.1093/molbev/msm229. PubMed DOI

Swofford DL. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4. Sinauer Associates, Sunderland, Massachusetts; 2002. PubMed

Philippe H. MUST, a computer package of management utilities for sequences and trees. Nucleic Acids Res. 1993;21:5264–5272. doi: 10.1093/nar/21.22.5264. PubMed DOI PMC

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. doi: 10.1093/bioinformatics/18.3.502. PubMed DOI

Stenzel DJ, Boreham PFL. Blastocystis hominis revisited. Clin Microbiol Rev. 1996;9:563–584. PubMed PMC

Tan KSW, Singh M, Yap EH. Recent advances in Blastocystis hominis research: hot spots in terra incognita. Int J Parasitol. 2002;32:789–804. doi: 10.1016/S0020-7519(02)00005-X. PubMed DOI

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. doi: 10.1093/nar/25.24.4876. PubMed DOI PMC

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.

Posada D, Crandall CA. MODELTEST: testing the model of DNA substitution. Bioinf. 1998;14:817–818. doi: 10.1093/bioinformatics/14.9.817. PubMed DOI

Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches