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