I'm trying to decide what would be the most appropriate threshold criteria?  In particular, this is for PFAMs and a human metagenomics dataset.  I'm curious what people have done in the past?  It looks like anvio uses --cut_ga as the default. https://github.com/merenlab/anvio/issues/498

**What been generally accepted as the most appropriate for metagenomics?** 



       --cut_ga
              Use Pfam GA (gathering threshold) score cutoffs.  Equivalent  to
              --globT <GA1> --domT <GA2>, but the GA1 and GA2 cutoffs are read
              from the HMM file. hmmbuild puts  these  cutoffs  there  if  the
              alignment file was annotated in a Pfam-friendly alignment format
              (extended SELEX or Stockholm format) and the optional GA annota-
              tion  line  was present. If these cutoffs are not set in the HMM
              file, --cut_ga doesn't work.


       --cut_tc
              Use Pfam  TC  (trusted  cutoff)  score  cutoffs.  Equivalent  to
              --globT <TC1> --domT <TC2>, but the TC1 and TC2 cutoffs are read
              from the HMM file. hmmbuild puts  these  cutoffs  there  if  the
              alignment file was annotated in a Pfam-friendly alignment format
              (extended SELEX or Stockholm format) and the optional TC annota-
              tion  line  was present. If these cutoffs are not set in the HMM
              file, --cut_tc doesn't work.


       --cut_nc
              Use Pfam NC (noise cutoff) score cutoffs. Equivalent to  --globT
              <NC1>  --domT  <NC2>,  but the NC1 and NC2 cutoffs are read from
              the HMM file. hmmbuild puts these cutoffs there if the alignment
              file was annotated in a Pfam-friendly alignment format (extended
              SELEX or Stockholm format) and the optional NC  annotation  line
              was  present.  If  these  cutoffs  are  not set in the HMM file,
              --cut_nc doesn't work.


http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=hmmsearch
As explained above, none of these options will matter unless your HMM has the cutoffs set. The appropriate lines in HMMs look like this:

    GA    25.00 25.00;
    TC    25.00 25.00;
    NC    24.90 24.90;

These bit-scores have to be set manually during model building, and their main purpose is to catch borderline matches that may be true hits but have statistically insignificant E-values. On rare occasions, the use of these cutoffs would eliminate a match that has barely significant E-value. A simple way of setting these scores is to pick the worst score in a known group of trusted family members.

Most of the time you will get the same result from these scores or from E-values, and I use the latter as a guide. It is good practice to manually inspect hits that are just above or just below the E-value threshold, and to set the database size (`-Z` switch) to a fixed number so that searches done over large period of time and with different databases can be compared. If you check [**how Pfam does it**][1], you will notice that they are not using cutoffs even though the HMMs support them. Instead, they set the database size to `45638612`.


  [1]: https://pfam.xfam.org/family/PF00041#tabview=tab6