hmmconvert man page

hmmconvert — convert profile file to a HMMER format

Synopsis

hmmconvert [options] <hmmfile>

Description

The hmmconvert utility converts an input profile file to different HMMER formats.

By default, the input profile can be in any HMMER format, including old/obsolete formats from HMMER2, ASCII or binary; the output profile is a current HMMER3 ASCII format.

<hmmfile> may be '-' (dash), which means reading this input from stdin rather than a file.

Options

-h
Help; print a brief reminder of command line usage and all available options.
-a
Output profiles in ASCII text format. This is the default.
-b
Output profiles in binary format.
-2
Output in legacy HMMER2 ASCII text format, in ls (glocal) mode. This allows HMMER3 models to be converted back to a close approximation of HMMER2, for comparative studies.
--outfmt <s>
Output in a HMMER3 ASCII text format other then the most current one. Valid choices for <s> are 3/a through 3/f. The current format is 3/f, and this is the default. The format 3/b was used in the official HMMER3 release, and the others were used in the various testing versions.

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 ().

Author

Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org

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Info

February 2015 HMMER 3.1b2 HMMER Manual