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LOCARNATE(1)	      User Contributed Perl Documentation	  LOCARNATE(1)

NAME
       locarnate

SYNOPSIS
       locarnate [--parwise_params <parameters>	--tcoffee_params <parameters>
		  --pp_calculater_params <parameters> --help
       --pairwise_aligner <locarna or exparnap>
		  --output <outputFolder> --library-only <lib-file>
       --library-name <name>
		  --additional-libraries <list_of_libraries>] <inputFile>

       Creates MSAs using different pairwise aligners and TCoffee as a
       multiple	alignment tool

AUTHORS
       Niklas Meinzer <meinzern@informatik.uni-freiburg.de

OPTIONS
       --pairwise_parameters
	   parameters for the pairwise alignment step

       --tcoffee_params
	   parameters for tcoffee

       --pp_calculator_params
	   parameters for locarna_rnafold_pp

       --output
	   path	to output folder

       --library-only
	   if  given  only  a  t-coffee	library	will be	written	without	actual
	   computation

       --library-name
	   the file name of the	produced t-coffee library
				       (default: "input.lib")

       --additional-libraries
	   a comma separated list of paths  to	t-coffee  library  files  that
	   should be given to t-coffee in addition to the one generated	during
	   this	run

       --pairwise_aligner
	   which pairwise aligner to use (default: locarna)

       --scaling_factor
	   each	edge from each EPM gets	the same weight	(exparnap only!)

       --help
	   display this	help message and exit

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

Want to link to this manual page? Use this URL:
<https://man.freebsd.org/cgi/man.cgi?query=locarnate&sektion=1&manpath=FreeBSD+Ports+15.0>

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