Hello,
I recently start using hmmer 3 more specifically hmmalign in hmmer it takes an hmm model already build by hmmbuild and a fasta file containing multiple sequences. Previously I used infernal for align rna (cmmalign) . I used to take the total bit scores to do some analysis. The question are there any bit score in the output of hmmer ?
if not is the bit score for any hmmer version available ? and which one ?
As far as I can tell 'hmmalign' does not output any scores, however you may find that the contacting the HMMER developers (hmmer@janelia.hhmi.org) helpful, since they will be able to tell you if there is a way of obtaining scores or if they plan adding scores in future.
Moreover, something good to know is, while building your own HMM, you can compute some cutoffs (e.g. "trusted cutoff") taking into account some min or max scores between your model and the sequences used to make it.
If you have this information in your hmm, hmmscan or hmmsearch are able to filter hits according to it.
As far as I can tell 'hmmalign' does not output any scores, however you may find that the contacting the HMMER developers (hmmer@janelia.hhmi.org) helpful, since they will be able to tell you if there is a way of obtaining scores or if they plan adding scores in future.