Software
XRate: a fast prototyping, training and annotation tool for phylo-grammars
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* Corresponding author: Ian Holmes ihh@berkeley.edu
1 Department of Bioengineering, University of California, Berkeley CA, USA
2 European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
3 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca NY, USA
BMC Bioinformatics 2006, 7:428 doi:10.1186/1471-2105-7-428
Published: 3 October 2006Abstract
Background
Recent years have seen the emergence of genome annotation methods based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists.
Results
We have developed an open source software tool, xrate, for working with reversible, irreversible or parametric substitution models combined with stochastic context-free grammars. xrate efficiently estimates maximum-likelihood parameters and phylogenetic trees using a novel "phylo-EM" algorithm that we describe. The grammar is specified in an external configuration file, allowing users to design new grammars, estimate rate parameters from training data and annotate multiple sequence alignments without the need to recompile code from source. We have used xrate to measure codon substitution rates and predict protein and RNA secondary structures.
Conclusion
Our results demonstrate that xrate estimates biologically meaningful rates and makes predictions whose accuracy is comparable to that of more specialized tools.