Bio::Phylo::Unparsers::Phylip - Serializer used by Bio::Phylo::IO, no serviceable parts inside
This module unparses a Bio::Phylo data structure into an input file for PHYLIP and RAxML. The file format (as it is interpreted here) consists of:
the number of species, a space, the number of characters
ten-character species name, sequence
Here is an example of what the output might look like:
4 2 Species_1 AC Species_2 AG Species_3 GT Species_4 GG
To the unparse() function pass a matrix object or a project (whose first matrix will be serialized) as value of the '-phylo' argument. After serialization, any shortened phylip-specific names (which need to be 10 characters long) will have been assigned to the 'phylip_name' slot of set_generic. Example:
my $phylip_string = unparse( -format => 'phylip', -phylo => $matrix, ); for my $seq ( @{ $matrix->get_entities } ) { # this returns the shortened name, which is unique to the matrix my $phylip_name = $seq->get_generic('phylip_name'); }
The phylip module is called by the Bio::Phylo::IO object, so look there to learn about parsing and serializing in general.
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The phylip 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
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.