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Author image Rutger Vos
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Bio::Phylo::Unparsers::Nwmsrdf - Serializer used by Bio::Phylo::IO, no serviceable parts inside


This unparser produces multistate character state matrices for the "Network" (http://www.fluxus-engineering.com/sharenet.htm) program. These files by Network's conventions have the .rdf extension, which has nothing to do with RDF. The matrices are represented as follows:

Only variable columns are shown. The header includes the column number.
The end of each character row has the frequency of the haplotype. By default this is 1, other values can be specified by adding an annotation to the row in question:
        $row->set_meta_object( 'bp:haplotype_frequency' => 2 );
The bottom of the file lists the weight of each column. By default this is 10, other values can be specified by adding a weight to the character:
        $char->set_weight( 15 );
Taxon names must be variable in the first 6 characters as they are truncated to this length.


There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.


The nwmsrdf unparser is called by the Bio::Phylo::IO object. Look there to learn how to create phylip formatted files.


Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.


If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63