1hmmlogo(1)                       HMMER Manual                       hmmlogo(1)
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NAME

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

11       hmmlogo [options] <hmmfile>
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DESCRIPTION

16       hmmlogo computes letter height and indel parameters that can be used to
17       produce a profile HMM logo. This tool  is  essentially  a  command-line
18       interface  for  much  of  the  data  underlying the Skylign logo server
19       (skylign.org).
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21       By default, hmmlogo prints out a table of per-position  letter  heights
22       (dependent on the requested height method), then prints a table of per-
23       position gap probabilities.
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25       In a typical logo, the total height of a stack of letters for one posi‐
26       tion depends on the information content of the position, and that stack
27       height is subdivided according to the  emission  probabilities  of  the
28       letters of the alphabet.
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OPTIONS

33       -h     Help;  print  a  brief  reminder  of  command line usage and all
34              available options.
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38       --height_relent_all
39              Total height = relative entropy (aka information  content);  all
40              letters are given a positive height.  (default)
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43       --height_relent_abovebg
44              Total  height = relative entropy (aka information content); only
45              letters with above-background  probability  are  given  positive
46              height.
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49       --height_score
50              Total  height = sums of scores of positive-scoring letters; let‐
51              ter height depends on the score of that letter at that position.
52              Only  letters with above-background probability (positive score)
53              are given positive height. (Note  that  only  letter  height  is
54              meaningful - stack height has no inherent meaning).
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57       --no_indel
58              Don't print out the indel probability table.
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SEE ALSO

63       See  hmmer(1)  for  a master man page with a list of all the individual
64       man pages for programs in the HMMER package.
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67       For complete documentation, see the user  guide  that  came  with  your
68       HMMER distribution (Userguide.pdf); or see the HMMER web page ().
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74       Copyright (C) 2015 Howard Hughes Medical Institute.
75       Freely distributed under the GNU General Public License (GPLv3).
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77       For  additional  information  on  copyright and licensing, see the file
78       called COPYRIGHT in your HMMER source distribution, or  see  the  HMMER
79       web page ().
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AUTHOR

84       Eddy/Rivas Laboratory
85       Janelia Farm Research Campus
86       19700 Helix Drive
87       Ashburn VA 20147 USA
88       http://eddylab.org
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95HMMER 3.1b2                      February 2015                      hmmlogo(1)
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