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| Bio::Phylo::Parsers::Phylip(3) | User Contributed Perl Documentation | Bio::Phylo::Parsers::Phylip(3) |
NAME
Bio::Phylo::Parsers::Phylip - Parser used by Bio::Phylo::IO, no serviceable parts insideDESCRIPTION
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>
| 2017-10-30 | perl v5.32.1 |
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