PARAMETERS

         This software is a terminal program that requires some optional parameters. The parameter '-f' followed by the name of the input file is the only obligatory parameter. Below there is the complete list of the parameters required to run topd/fMtS.

             - Input file name: -f file_name
             - Methods: -m nodal/split/quartets/triplets/disagree/all (default: split)
             - Number of triplets&quartets -u all/random/relative (default: all)
             - Random analysis: -r random/guided/no (default: random)
             - Number of random trees: -n 1-1000 (default: 100)
             - Number of fMtS trees: -s 10-10000/all/relative (default: relative)
             - Type of comparison: -c single/multiple/reference (default: single)
             - Disagree level: -l 1/2/3/4 (default: 1)
             - Print previous results: -p y/n (default: yes)

         Extra features of this software:

             - Get species form trees: -species file_name
             - Prune trees: -prune file_trees file_sp_to_prune
             - FMTS trees: -fmts file_trees
             - Get quartets: -quartets file_trees
             - Get triplets: -triplets file_trees
             - Duplidist: -dd file_trees
             - Quickquartets: -qq file_trees number_quartets
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