NAME

Bio::Phylo::Unparsers::Newick - Unparses newick trees. 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

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.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Newick.pm 4193 2007-07-11 20:26:06Z rvosa $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.