SYNOPSIS
cmconvert [options] <cmfile>
DESCRIPTION
The cmconvert utility converts an input covariance model file to different Infernal formats.
By default, the input CM file can be any CM file created by Infernal version 1.0 or later; the output CM file is a current Infernal format. Files from versions older than version 1.0 cannot be converted.
<cmfile> 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.
- -1
-
Output in legacy Infernal1 (Infernal v1.0 through v1.0.2) ASCII text
format. Due to important changes between version v1.0.2 and v1.1, any
E-value statistic parameters calculated by
cmcalibrate
in
<cmfile>
will not be written to the converted output file.
- --mlhmm
-
Do not output a CM file. Instead, output one maximum likelihood p7 HMM
built from each CM in
<cmfile>
in HMMER3 ASCII text format. The HMM will have been constructed to be
as similar as possible to the CM, without modeling secondary
structure. This option could be useful for comparative studies of
Infernal and HMMER3.
- --fhmm
-
Do not output a CM file. Instead, output the filter p7 HMM
for each CM in
<cmfile>
in HMMER3 ASCII text format.
COPYRIGHT
Copyright (C) 2014 Howard Hughes Medical Institute. Freely distributed under the GNU General Public License (GPLv3).
For additional information on copyright and licensing, see the file called COPYRIGHT in your Infernal source distribution, or see the Infernal web page ().
AUTHOR
The Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org