xrate: A Tool for Phylo-Grammars
Author Information
Author(s): Peter S Klosterman, Andew V Uzilov, Yuri R Bendaña, Robert K Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman, Ian Holmes
Primary Institution: University of California, Berkeley
Hypothesis
Can xrate efficiently estimate maximum-likelihood parameters and phylogenetic trees using a novel phylo-EM algorithm?
Conclusion
xrate estimates biologically meaningful rates and makes predictions whose accuracy is comparable to that of more specialized tools.
Supporting Evidence
- xrate can handle a broad class of phylo-grammars within one framework.
- xrate's performance is comparable to previously described phylo-HMM and phylo-SCFG implementations.
- xrate allows users to design new grammars and annotate multiple sequence alignments without recompiling code.
- xrate has been used to measure codon substitution rates and predict protein and RNA secondary structures.
Takeaway
xrate is a software tool that helps scientists quickly analyze genetic data by estimating rates of changes in DNA and RNA sequences.
Methodology
Developed an open source software tool for estimating parameters and phylogenetic trees using a phylo-EM algorithm.
Limitations
The automated parameterization of phylo-grammars from training data is still somewhat uncharted territory.
Statistical Information
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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