Indel-based evolutionary distance and mouse-human divergence.

@article{Ogurtsov2004IndelbasedED,
  title={Indel-based evolutionary distance and mouse-human divergence.},
  author={Aleksey Y. Ogurtsov and Shamil R. Sunyaev and Alexey S. Kondrashov},
  journal={Genome research},
  year={2004},
  volume={14 8},
  pages={1610-6}
}
We propose a method for estimating the evolutionary distance between DNA sequences in terms of insertions and deletions (indels), defined as the per site number of indels accumulated in the course of divergence of the two sequences. We derive a maximal likelihood estimate of this distance from differences between lengths of orthologous introns or other segments of sequences delimited by conservative markers. When indels accumulate, lengths of orthologous introns diverge only slightly slower… CONTINUE READING

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