I'm trying to implement a Dirichlet mixture model for computing HMM emission probabilities, based on the paper by Sjolander et al 1996. My program seems to be working OK, but to be sure that my code is free of bugs I would like to compare it to the output of hmmbuild algorithm (HMMER 3), which uses Dirichlet mixture model for computing HMM emission probabilities as a default.
As far as I understand HMMER 3 uses a new Dirichlet prior, not the one from []? So could someone please tell me where can I get the new Dirichlet mixture parameters for HMMER 3. HMMER 3.1 manual says only that Dirichlet mixture prior parameters are "built in".