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cmconvert(1)			Infernal Manual			  cmconvert(1)

NAME
       cmconvert - convert Infernal covariance model files

SYNOPSIS
       cmconvert [options] _cmfile_

DESCRIPTION
       The  cmconvert  utility converts	an input covariance model file to dif-
       ferent 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  for-
	      mat. The HMM will	have been constructed to be as similar as pos-
	      sible to the CM, without modeling	secondary structure. This  op-
	      tion could be useful for comparative studies of Infernal and HM-
	      MER3.

       --fhmm Do not output a CM file. Instead,	output the filter p7  HMM  for
	      each CM in <cmfile> in HMMER3 ASCII text format.

SEE ALSO
       See infernal(1) 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  In-
       fernal distribution (Userguide.pdf); or see the Infernal	web page ().

COPYRIGHT
       Copyright (C) 2019 Howard Hughes	Medical	Institute.
       Freely distributed under	the BSD	open source license.

       For  additional	information  on	 copyright and licensing, see the file
       called COPYRIGHT	in your	Infernal source	distribution, or see  the  In-
       fernal web page ().

AUTHOR
       The Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147	USA
       http://eddylab.org

Infernal 1.1.3			   Nov 2019			  cmconvert(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT | AUTHOR

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