hmmlogo(1) given an HMM, produce data required to build an HMM logo


hmmlogo [options] <hmmfile>


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 (

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.


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

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

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

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).

Don't print out the indel probability table.


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 ().


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