Rutger Vos > Bio-Phylo-0.56 > Bio::Phylo::Parsers::Phylip

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NAME ^

Bio::Phylo::Parsers::Phylip - Parser used by Bio::Phylo::IO, no serviceable parts inside

DESCRIPTION ^

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;

SEE ALSO ^

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

Bio::Phylo::IO

The PHYLIP parser is called by the Bio::Phylo::IO object. Look there for examples.

Bio::Phylo::Manual

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

CITATION ^

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

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