Hi All,

I am new to HyPhy batch language.

I was wondering if there's a simple way to edit nucmodelcompare.bf, in order to compare not only the 203 GTR submodels, but the full 812 submodels of GTR+I+G (i.e. each of the 203 models, with all combinations of +I and +G)?

Thanks

Rob

Hi Rob,

nucmodelcompare.bf is a bit of a beast, so I would not recommend trying to modify it directly.
If you are simply after the single best model, I would suggest that you test for +G, +I, +I+G FOLLOWING the model selection (among the 203). For that you can write a simple wrapper file to AnalyzeNucData.bf with custom model (6-characters) and differing rate variation options i.e. something along the lines of the attached file.

Sergei

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