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

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 the Bio::Phylo::IO manpage 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

the Bio::Phylo::IO manpage

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

the Bio::Phylo::Manual manpage

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

REVISION

 $Id: Newick.pm 1171 2009-07-07 06:23:58Z rvos $
 Bio::Phylo::Unparsers::Newick - Serializer used by Bio::Phylo::IO, no serviceable parts inside