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Bio::Phylo::Parsers::NUserkContributed Perl DocuBio::Phylo::Parsers::Newick(3)

       Bio::Phylo::Parsers::Newick - Parser used by Bio::Phylo::IO, no
       serviceable parts inside

       This module parses tree descriptions in parenthetical format. It	is
       called by the Bio::Phylo::IO facade, don't call it directly. Several
       additional flags	can be passed to the Bio::Phylo::IO parse and
       parse_tree functions to influence how to	deal with complex newick

	-keep => [ ...list of taxa names... ]

       The "-keep" flag	allows you to only retain certain taxa of interest,
       ignoring	others while building the tree object.

	-ignore_comments => 1,

       This will treat comments	in square brackets as if they are a normal
       taxon name character, this so that names	such as	"Choristoneura
       diversana|BC ZSM	Lep 23401[05/*"	are parsed "successfully". (Note:
       square brackets should NOT be used in this way as it will break many

	-keep_whitespace => 1,

       This will treat unescaped whitespace as if it is	a normal taxon name
       character. Normally, whitespace is only retained	inside quoted strings
       (e.g. 'Homo sapiens'), otherwise	it is the convention to	use
       underscores ("Homo_sapiens"). This is because some programs introduce
       whitespace to prettify a	newick string, e.g. to indicate
       indentation/depth, in which case	you almost certainly want to ignore
       it. This	is the default behaviour. The option to	keep it	is provided
       for dealing with	incorrectly formatted data.

       There is	a mailing list at
       <!forum/bio-phylo> for any user	or
       developer questions and discussions.

	   The newick parser is	called by the Bio::Phylo::IO object.  Look
	   there to learn how to parse newick strings.

	   Also	see the	manual:	Bio::Phylo::Manual and

       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.  <>

perl v5.32.1			  2017-10-13	Bio::Phylo::Parsers::Newick(3)


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