Bio::Phylo::Parsers::Phylip - Parser used by Bio::Phylo::IO, no serviceable parts inside
This module is used for parsing PHYLIP character state matrix files. At present this only works on non-interleaved files. As PHYLIP files don't indicate what data type they are you should indicate this as an argument to the Bio::Phylo::IO::parse function, i.e.:
use Bio::Phylo::IO 'parse'; my $file = shift @ARGV; my $type = 'dna'; # or rna, protein, restriction, standard, continuous my $matrix = parse( '-file' => $file, '-format' => 'phylip', '-type' => $type, )->[0]; print ref($matrix); # probably prints Bio::Phylo::Matrices::Matrix;
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The PHYLIP parser is called by the Bio::Phylo::IO object. Look there for examples.
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.