hmmconvert1

Usage

Overview

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.