Hi everyone,

I am using the hmmbuild function of the HMMER3.1 software to construct profile HMMs from multiple sequence alignments. I know that in HMMER2.2, the default profile architecture construction algorithm (that is, the algorithm that decides which MSA columns will become the match states) is a maximum a posteriori (MAP) approach, because this is mentioned in the manual. However, the manual of HMMER3.1 mentions that its default profile construction algorithm is a "fast" one where the percentage of non-gap residues in the column is compared to a threshold value.

So I have two questions:

- Is it possible to do MAP profile construction in HMMER3.1?
- If not, why did they remove that option?

Thanks in advance.