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Author image Rutger Vos
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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 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.


There is a mailing list at https://groups.google.com/forum/#!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 http://rutgervos.blogspot.com.


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