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  HyPhy Documentation: Miscellaneous: Deletions and Ambiguities

    HYPHY treats deletions in the data in one of two possible ways:

  • Keep Deletions: Deletions are treated as complete unknowns. In case of codons, data like A-T will be treated as A?T (i.e. either AAT, ACT, AGT or ATT).
  • Skip Deletions: Any site which contains at least one deletion will be excluded from the analysis. In case of codons, data like A-T will result in all 3 data columns being skipped.

    In general, HYPHY treats ambiguities by averaging over all possible translations, both in likelihood evaluation and in frequency gathering.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002