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BioPerl-1.007002
River stage two • 60 direct dependents • 65 total dependents
/ Bio::TreeIO::nexus

NAME

Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP

SYNOPSIS

use Bio::TreeIO;
my $in = Bio::TreeIO->new(-file => 't/data/cat_tre.tre');
while( my $tree = $in->next_tree ) {
}

DESCRIPTION

This is a driver module for parsing PAUP Nexus tree format which basically is just a remapping of trees.

Comments

The nexus format allows node comments that are placed inside square brackets. Usually the comments (implemented as tags for nodes) are used to give a name for an internal node or record the bootstrap value, but other uses are possible.

The FigTree program by Andrew Rambaut adds various rendering parameters inside comments and flags these comments by starting them with '&!'. The parameters implemented here are 'label' and 'color'.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-open-bio-dot-org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Args    : -header    => boolean  default is true 
                        print/do not print #NEXUS header
          -translate => boolean default is true
                        print/do not print Node Id translation to a number

next_tree

Title   : next_tree
Usage   : my $tree = $treeio->next_tree
Function: Gets the next tree in the stream
Returns : Bio::Tree::TreeI
Args    : none

write_tree

Title   : write_tree
Usage   : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args    : Bio::Tree::TreeI
Title   : header
Usage   : $obj->header($newval)
Function: 
Example : 
Returns : value of header (a scalar)
Args    : on set, new value (a scalar or undef, optional)

translate_node

Title   : translate_node
Usage   : $obj->translate_node($newval)
Function: 
Example : 
Returns : value of translate_node (a scalar)
Args    : on set, new value (a scalar or undef, optional)