HMMER User's Guide

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hmmconvert - convert between profile HMM file formats

Synopsis

hmmconvert [options] oldhmmfile newhmmfile

Description

hmmconvert reads an HMM file from oldhmmfile in any HMMER format, and writes it to a new file newhmmfile in a new format. oldhmmfile and newhmmfile must be different files; you can't reliably overwrite the old file. By default, the new HMM file is written in HMMER 2 ASCII format.

Available formats are HMMER 2 ASCII (default), HMMER 2 binary (-b) GCG profile (-p) , and Compugen XSW extended profile (-P).

Options

• [-a ] Convert to HMMER 2 ASCII file. This is the default, so this option is unnecessary.

• [-b ] Convert to HMMER 2 binary file.

• [-h ] Print brief help; includes version number and summary of all options, including expert options.

• [-p ] Convert to GCG profile .prf format.

• [-A ] Append mode; append to newhmmfile rather than creating a new file.

• [-F ] Force; if newhmmfile already exists, and -A is not being used to append to the file, hmmconvert will refuse to clobber the existing file unless -F is used.

• [-P ] Convert the HMM to Compugen XSW extended profile format, which is similar to GCG profile format but has two extra columns for delete-open and delete-extend costs. (I do not believe that Compugen publicly supports this format; it may be undocumented.)