Bio::PhyloTastic::TaxTractor - Extracts taxa from phylogenetic file formats
phylotastic TaxTractor -i <infile> -d nexml -o <outfile> -search '_' -r ' '
This module extracts taxon labels from common phylogenetic file formats.
An input file. Default is a text file with one name per line. Required.
An output file name. If '-', prints output to STDOUT. Required.
An input format, such as NEXUS, Newick, NeXML, PhyloXML, TaxList. Required.
An output format, such as NeXML, TaxList. Optional. Default is TaxList (i.e. a simple text file).
A character (or pattern) to search for, which is replaced with the -r argument. This is especially useful for replacing underscores (which occur often) with spaces.
What the value of -search gets replaced with.