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)