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LOCARNA_MCC(1)	      User Contributed Perl Documentation	LOCARNA_MCC(1)

NAME
       locarna_mcc

SYNOPSIS
       locarna_mcc -f=<annotation_file>	[options] aln_file(s)

       Computes	the MCC	(Mathew's correlation coefficient) along with several
       other secondary structure prediction performance	measures for
       structures predicted by RNAalifold from one or several alignments in
       CLUSTAL W format.

       Options:

       -f=<annotation_file>
	    Structure annotation file. Mandatory argument.

       -P=<param_file>
	    Parameter file for RNAalifold

       --alifold-args
	    Alifold arguments (default:	same as	mlocarna)

       --assume-fasta
	    Assume that	input is in fasta format (instead of clustalw aln)

       --help
	    Brief help message

       --man
	    Full documentation

       -v, --verbose
	    Verbose

       -q, --quiet
	    Quiet

DESCRIPTION
       For  each  file produce an output line <name> <tp> <fp> <fn> <tn> <ppv>
       <sens> <mcc> <sqrt($sens*$ppv)>

       The structure annotation	 file  contains	 lines	of  <name>  <sequence>
       <structure>  and	 must  contain	an  entry  for	each  sequence	in the
       alignment.

perl v5.32.1			  2022-11-19			LOCARNA_MCC(1)

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