hmmlogo man page

hmmlogo — 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.

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 ().


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Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA


February 2015 HMMER 3.1b2 HMMER Manual