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