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.
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 bootstap 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://redmine.open-bio.org/projects/bioperl/
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)