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why use TN93 mode not others? #35

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liamxg opened this issue Nov 14, 2023 · 2 comments
Open

why use TN93 mode not others? #35

liamxg opened this issue Nov 14, 2023 · 2 comments

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@liamxg
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liamxg commented Nov 14, 2023

Is this the best mode for genetic distance? @stevenweaver @spond

@spond
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spond commented Nov 14, 2023

Dear @liamxg,

There is no best genetic distance. The TN93 distance has a simple closed-form expression, i.e. you can compute it from pairwise counts. You can't do it for more complex models (e.g. REV). Simpler models, like K2P, are poor choices for HIV-1, because it has strong compositional biases (e.g. A ~ 40%). One reference that I recall is https://pubmed.ncbi.nlm.nih.gov/15750402/

For small distances (e.g. <1%), there is generally little difference between the actual model used, but we might as well keep a realistic model in place.

Best,
Sergei

@liamxg
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liamxg commented Nov 14, 2023

Thank for your reply, could we do model selection first for each dataset, and use the optimal model to calculate the genetic distance?

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