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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>  <struc-
     ture> and must contain an entry for each sequence in the alignment.

perl v5.38.2			   2022-10-04			  LOCARNA_MCC(1)

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