Abstract
BackgroundSlow-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.ResultsOur 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.ConclusionSlowFaster 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.
Highlights
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
Sample Data As an example, we analysed an alignment of 34 SSU rDNA sequences of 31 isolates of Blastocystis + 3 outgroups
These nonflagellated, multinucleated gut commensals comprise a single genus, their SSU rDNA phylogeny shows clearly that they are rather long branched taxa in comparison to other stramenopiles. Their branches are even longer than, for example, branches separating classes of autotrophic stramenopiles. This group is suspected of a high level of substitution saturation
Summary
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. It goes through the whole process in several steps: data input – necessary choices – production of new alignments
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