locarnate

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 <meinz.nosp@m.ern@.nosp@m.infor.nosp@m.mati.nosp@m.k.uni.nosp@m.-fre.nosp@m.iburg.nosp@m..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