hmmstat man page

hmmstat — display summary statistics for a profile file


hmmstat [options] <hmmfile>


The hmmstat utility prints out a tabular file of summary statistics for each profile in <hmmfile>.

<hmmfile> may be '-' (a dash character), in which case profiles are read from a <stdin> pipe instead of from a file.

The columns are:

The index of this profile, numbering each on in the file starting from 1.
The name of the profile.
The optional accession of the profile, or "-" if there is none.
The number of sequences that the profile was estimated from.
The effective number of sequences that the profile was estimated from, after HMMER applied an effective sequence number calculation such as the default entropy weighting.
The length of the model in consensus residues (match states).
Mean relative entropy per match state, in bits. This is the expected (mean) score per consensus position. This is what the default entropy-weighting method for effective sequence number estimation focuses on, so for default HMMER3 models, you expect this value to reflect the default target for entropy-weighting.
Mean information content per match state, in bits. Probably not useful. Information content is a slightly different calculation than relative entropy.
p relE
Mean positional relative entropy, in bits. This is a fancier version of the per-match-state relative entropy, taking into account the transition (insertion/deletion) probabilities; it may be a more accurate estimation of the average score contributed per model consensus position.
Kullback-Leibler distance between the model's overall average residue composition and the default background frequency distribution. The higher this number, the more biased the residue composition of the profile is. Highly biased profiles can slow the HMMER3 acceleration pipeline, by causing too many nonhomologous sequences to pass the filters.


Help; print a brief reminder of command line usage and all available options.

See Also

See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package.

For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page ().


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