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cmconvert - Online in the Cloud

Run cmconvert in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command cmconvert that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


cmconvert - convert Infernal covariance model files

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.

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