Dear Konrad,

HyPhy core does not make any assumptions which rely on time reversibility, hence you can specify non-reversible models in the batch language and the calculations will be correct. The only assumption (which you can override with the ACCEPT_ROOTED_TREES = 1 flag in the code) is that trees can be 'unrooted' and 'rerooted' at will - rerooting a tree will, in general, change the results under a non-reversible model.

Cheers,
Sergei