Learning to count: robust estimates for labeled distances between molecular sequences.

@article{OBrien2009LearningTC,
  title={Learning to count: robust estimates for labeled distances between molecular sequences.},
  author={John D. O'Brien and Vladimir N. Minin and Marc A. Suchard},
  journal={Molecular biology and evolution},
  year={2009},
  volume={26 4},
  pages={
          801-14
        }
}
Researchers routinely estimate distances between molecular sequences using continuous-time Markov chain models. We present a new method, robust counting, that protects against the possibly severe bias arising from model misspecification. We achieve this robustness by generalizing the conventional distance estimation to incorporate the empirical distribution of site patterns found in the observed pairwise sequence alignment. Our flexible framework allows for computing distances based only on a… CONTINUE READING
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