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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 (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.


-h 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.

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