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hmmlogo(1)			 HMMER Manual			    hmmlogo(1)

NAME
       hmmlogo - produce a conservation	logo graphic from a profile

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 in-
       terface	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 posi-
       tion 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; let-
	      ter 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  HM-
       MER distribution	(Userguide.pdf); or see	the HMMER web page (http://hm-
       mer.org/).

COPYRIGHT
       Copyright (C) 2019 Howard Hughes	Medical	Institute.
       Freely distributed under	the BSD	open source license.

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

AUTHOR
       http://eddylab.org

HMMER 3.3			   Nov 2019			    hmmlogo(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT | AUTHOR

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