TrN (df = k+5) and TrNe (df = k+2) - which of these Tamura-Nei model variants is used in MEGAx?
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11 months ago
poecile.pal ▴ 50

Good morning,

I have used modelTest {phangorn} to test different nucleotide substitution models. There are 2 variants of Tamura-Nei model in it's output, which have differences in the number of degrees of freedom: TrNe has k+2 free parameters, TrN has k+5 free parameters.

In MEGAx I see only one variant - "Tamura-Nei". But TrNe and TrN have different AIC, BIC.

Could you please explain if "Tamura-Nei" in MEGAx corresponds to TrNe or Trn in modelTest {phangorn}?

Best regards, Poecile

Tamura-Nei phylogeny phangorn modelTest mega • 295 views

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