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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 compu-
	 tation

     --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 v5.38.2			   2022-10-04			    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+15.1.quarterly>

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