hmmconvert - Man Page

convert profile file to a HMMER format


hmmconvert [options] <hmmfile>


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.  



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


Output profiles in ASCII text format. This is the default.


Output profiles in binary format.


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 ().


Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA



February 2015 HMMER 3.1b2 HMMER Manual