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>.

       <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 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 ().

COPYRIGHT

       Copyright (C) 2013 Howard Hughes Medical Institute.
       pFreely distributed under the GNU General Public License (GPLv3).

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

AUTHOR

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