Rutger Vos > Bio-Phylo-0.56 > Bio::Phylo::Unparsers::Newick

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NAME ^

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

DESCRIPTION ^

This module turns a tree object into a newick formatted (parenthetical) tree description. It is called by the Bio::Phylo::IO facade, don't call it directly. You can pass the following additional arguments to the unparse call:

        # by default, names for tips are derived from $node->get_name, if 
        # 'internal' is specified, uses $node->get_internal_name, if 'taxon'
        # uses $node->get_taxon->get_name, if 'taxon_internal' uses 
        # $node->get_taxon->get_internal_name, if $key, uses $node->get_generic($key)
        -tipnames => one of (internal|taxon|taxon_internal|$key)
        
        # for things like a translate table in nexus, or to specify truncated
        # 10-character names, you can pass a translate mapping as a hashref.
        # to generate the translated names, the strings obtained following the
        # -tipnames rules are used.
        -translate => { Homo_sapiens => 1, Pan_paniscus => 2 }  
        
        # array ref used to specify keys, which are embedded as key/value pairs (where
        # the value is obtained from $node->get_generic($key)) in comments, 
        # formatted depending on '-nhxstyle', which could be 'nhx' (default), i.e.
        # [&&NHX:$key1=$value1:$key2=$value2] or 'mesquite', i.e. 
        # [% $key1 = $value1, $key2 = $value2 ]
        -nhxkeys => [ $key1, $key2 ]    
        
        # if set, appends labels to internal nodes (names obtained from the same
        # source as specified by '-tipnames')
        -nodelabels => 1
        
        # specifies a formatting style / dialect
        -nhxstyle => one of (mesquite|nhx)
        
        # specifies a branch length sprintf number formatting template, default is %f
        -blformat => '%e'

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 newick unparser is called by the Bio::Phylo::IO object. Look there to learn how to unparse newick strings.

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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