NAME

       hmmlogo - given an HMM, produce data required to build an HMM logo

SYNOPSIS

       hmmlogo [options] <hmmfile>

DESCRIPTION

       hmmlogo  computes letter height and indel parameters that can be used to produce a profile
       HMM logo. This tool  is  essentially  a  command-line  interface  for  much  of  the  data
       underlying the Skylign logo server (skylign.org).

       By  default,  hmmlogo  prints out a table of per-position letter heights (dependent on the
       requested height method), then prints a table of per-position gap probabilities.

       In a typical logo, the total height of a stack of letters for one position depends on  the
       information  content of the position, and that stack height is subdivided according to the
       emission probabilities of the letters of the alphabet.

OPTIONS

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

       --height_relent_all
              Total height = relative entropy (aka information content); all letters are given  a
              positive height.  (default)

       --height_relent_abovebg
              Total height = relative entropy (aka information content); only letters with above-
              background probability are given positive height.

       --height_score
              Total height = sums of scores of positive-scoring letters; letter height depends on
              the  score  of  that  letter  at  that position. Only letters with above-background
              probability (positive score) are given positive  height.  (Note  that  only  letter
              height is meaningful - stack height has no inherent meaning).

       --no_indel
              Don't print out the indel probability table.

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) 2015 Howard Hughes Medical Institute.
       Freely 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