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Allow user to specify how selective effects combine in overlapping regions #126

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ArtPoon opened this issue Jan 12, 2023 · 1 comment
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@ArtPoon
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ArtPoon commented Jan 12, 2023

  • we assume that selection on non-synonymous substitutions (dN) in overlapping ORFs combine multiplicatively, such that the net effect on substitution rate is w1 * w2 (where w1 is the effect in ORF1 and w2 is in ORF2)
  • this is not necessarily the case and there are other ways of combining effects, such as additive (w1 + w2)
  • we have to make the assumption that being one or the other applies globally to all sites
  • one other method would be a weighted sum, where the user would have to specify an "importance factor" for each ORF
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ArtPoon commented Mar 28, 2023

@SandeepThokala please coordinate with @horaciobam

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