Bio::PhyloTastic::PhyleMerge - Merges contents of phylogenetic data files
phylotastic PhyleMerge -i <file1> -d <format1> \ -i <file2> -d <format2> -o <outfile> -w '_' -u 1 -p 2
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).
An input file. Required. Can be used multiple times.
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).
An output file name. If '-', prints output to STDOUT. Required.
An output format, including NeXML, TaxList. Required.
Replaces <arg> with whitespace before attempting to join taxon labels.
If true, strips single and double quotes before attempting to join taxon labels.
Strips taxon labels down to the first <num> words (e.g. 2 for binomials) before attempting to join taxon labels.
To install Bio::PhyloTastic, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::PhyloTastic
CPAN shell
perl -MCPAN -e shell install Bio::PhyloTastic
For more information on module installation, please visit the detailed CPAN module installation guide.