NAME

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

SYNOPSIS

use Bio::TreeIO;
my $in = new Bio::TreeIO(-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.

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

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:

http://bugzilla.open-bio.org/

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

header

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)