Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins.

@article{Heger2009AccurateEO,
  title={Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins.},
  author={Andreas Heger and Chris Paul Ponting and Ian Holmes},
  journal={Molecular biology and evolution},
  year={2009},
  volume={26 8},
  pages={
          1715-21
        }
}
XRATE implements algorithms for comparative annotation, ancestral reconstruction, evolutionary rate estimation, and simulation. Its modeling repertoire includes phylogenetic stochastic context-free grammars and phylo-hidden Markov models. Following earlier tests of XRATE as a machine-learning tool suitable for alignment annotation, we now report the first tests of XRATE as a precise quantitative instrument for estimating evolutionary rates. We implement a codon model similar to that of Goldman… CONTINUE READING

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