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Bio::Phylo::Unparsers:UseriContributed Perl DoBio::Phylo::Unparsers::Newick(3)

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>

perl v5.32.1			  2017-10-30  Bio::Phylo::Unparsers::Newick(3)

NAME | DESCRIPTION | SEE ALSO | CITATION

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