Substitution mapping

[Shea Lambert]

Hello,

I'd like to use bppml and testNH to replicate the substitution mapping procedure of Romiguier et al. 2012 and Figuet et al. 2016.

However, it seems as though the example files for this procedure from Romiguier et al. 2012 (MitoMammals) provided with version 1.1.0 of testNH are outdated (e.g., the params files use old arguments "type" and "useObservedFreqs"). I've tried to update the files as best I can, and believe I have bppML fitting a YN98 model correctly, but the documentation for TestNH 1.10 [http://biopp.univ-montp2.fr/manual/pdf/testnh/v1.1.0/testnh.pdf] provides no information on certain 'missing' parameters, such as nullModelParams (which I've taken to be the estimated Y98 parameters from bppml). I don't think I can be sure that I'm running the procedure entirely correctly, though. Any advice (or an example control file) would be much appreciated!

Thanks,

Shea Lambert