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

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

DESCRIPTION
       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
       strings:

	-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
       parsers).

	-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.

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 parser is	called by the Bio::Phylo::IO object.  Look
	   there to learn how to parse 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			  2017-10-13	Bio::Phylo::Parsers::Newick(3)

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