NAME

       hmmstat - 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.

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

       The columns are:

       idx    The index of this profile, numbering each profile 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  divergence  from  the  default  background frequency distribution to the average
              composition of the profile's consensus match states, in bits.  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 (http://hmmer.org/).

COPYRIGHT

       Copyright (C) 2019 Howard Hughes Medical Institute.
       Freely distributed under the BSD open source license.

       For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source
       distribution, or see the HMMER web page (http://hmmer.org/).

AUTHOR

       http://eddylab.org