xenial (1) hmmstat.1.gz

Provided by: hmmer_3.1b2-2_amd64 bug

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 (C) 2015 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