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Manual Reference Pages  -  BIO::PHYLO::UNPARSERS::PHYLIP (3)

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NAME

Bio::Phylo::Unparsers::Phylip - Serializer used by Bio::Phylo::IO, no serviceable parts inside

CONTENTS

DESCRIPTION

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:
first line the number of species, a space, the number of characters
subsequent lines 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.

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

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::UNPARSERS::PHYLIP (3) 2014-02-08

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