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hmmstat(1)                       HMMER Manual                       hmmstat(1)


NAME

       hmmstat - display summary statistics for a profile file


SYNOPSIS

       hmmstat [options] <hmmfile>


DESCRIPTION

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

       The columns are:

       idx    The index of this profile, numbering each on in the file
              starting from 1.

       name   The name of the profile.

       accession
              The optional accession of the profile, or "-" if there is none.

       nseq   The number of sequences that the profile was estimated from.

       eff_nseq
              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.

       M      The length of the model in consensus residues (match states).

       relent 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.

       info   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.

       compKL 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.


OPTIONS

       -h     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
       (@HMMER_URL@).


COPYRIGHT

       @HMMER_COPYRIGHT@
       p@HMMER_LICENSE@

       For additional information on copyright and licensing, see the file
       called COPYRIGHT in your HMMER source distribution, or see the HMMER
       web page (@HMMER_URL@).


AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org

HMMER @HMMER_VERSION@            @HMMER_DATE@                       hmmstat(1)

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