Rutger Vos
and 1 contributors

NAME

Bio::PhyloTastic::TaxTractor - Extracts taxa from phylogenetic file formats

SYNOPSIS

 phylotastic TaxTractor -i <infile> -d nexml -o <outfile> -search '_' -r ' '

DESCRIPTION

This module extracts taxon labels from common phylogenetic file formats.

OPTIONS AND ARGUMENTS

-i infile

An input file. Default is a text file with one name per line. Required.

-o outfile

An output file name. If '-', prints output to STDOUT. Required.

-d informat

An input format, such as NEXUS, Newick, NeXML, PhyloXML, TaxList. Required.

-s outformat

An output format, such as NeXML, TaxList. Optional. Default is TaxList (i.e. a simple text file).

-search pattern

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.

-r character

What the value of -search gets replaced with.