Rutger Vos
and 1 contributors

NAME

Bio::PhyloTastic::PhyleMerge - Merges contents of phylogenetic data files

SYNOPSIS

 phylotastic PhyleMerge -i <file1> -d <format1> \
        -i <file2> -d <format2> -o <outfile> -w '_' -u 1 -p 2

DESCRIPTION

This module merges the contents of commonly encountered phylogenetic data formats. The module attempts to 'join' on taxon labels from the different files, optionally after pre-processing the labels, e.g. by removing quotes, replacing underscores with spaces and stripping away name suffixes (such as accessions).

OPTIONS AND ARGUMENTS

-i infile

An input file. Required. Can be used multiple times.

-d informat

An input format, such as NEXUS, Newick, NeXML, PhyloXML, TaxList. Required. Can be used multiple times (in which case the order must match those of the input files).

-o outfile

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

-s outformat

An output format, including NeXML, TaxList. Required.

-w <arg>

Replaces <arg> with whitespace before attempting to join taxon labels.

-u 1

If true, strips single and double quotes before attempting to join taxon labels.

-p <num>

Strips taxon labels down to the first <num> words (e.g. 2 for binomials) before attempting to join taxon labels.