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

HMMER 3.1b2                                       February 2015                                       hmmlogo(1)