Dataset Information

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

ABSTRACT:

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.

SUBMITTER: Kostka M

PROVIDER: S-EPMC2529323 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature

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Publications

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

Kostka Martin M Uzlikova Magdalena M Cepicka Ivan I Flegr Jaroslav J

BMC bioinformatics 20080815

<h4>Background</h4>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.<h4>Results</h4>Our program SlowFaster automates the process of assessing the substitution rate of the align ...[more]

PMID: 18702831

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Dataset Information

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

Background

Results

Conclusion

Publications

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

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