Software
SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis
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* Corresponding author: Martin Kostka mkostka@centrum.cz
1 Department of Parasitology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
2 Department of Anatomy and Physiology of Farm Animals, Faculty of Agriculture, University of South Bohemia in Ceske Budejovice, Studentska 13, 370 05 Ceske Budejovice, Czech Republic
3 Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
4 Department of Philosophy and History of Science, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
BMC Bioinformatics 2008, 9:341 doi:10.1186/1471-2105-9-341
Published: 15 August 2008Abstract
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.