cmconvert - convert Infernal covariance model files
cmconvert [options] <cmfile>
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.
may be '-' (dash), which means reading this input from
rather than a file.
- Help; print a brief reminder of command line usage and all
- Output profiles in ASCII text format. This is the default.
- Output profiles in binary format.
- 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.
- 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.
- Do not output a CM file. Instead, output the filter p7 HMM
for each CM in <cmfile> in HMMER3 ASCII text format.
for a master man page with a list of all the individual
man pages for programs in the Infernal package.
For complete documentation, see the user guide that came with your Infernal
distribution (Userguide.pdf); or see the Infernal web page ().
Copyright (C) 2016 Howard Hughes Medical Institute.
Freely distributed under a BSD open source license.
For additional information on copyright and licensing, see the file called
COPYRIGHT in your Infernal source distribution, or see the Infernal web page
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