Bio::TreeIO::nexus man page on Pidora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Pidora logo
[printable version]

Bio::TreeIO::nexus(3) User Contributed Perl DocumentationBio::TreeIO::nexus(3)

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 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:

	 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)

perl v5.14.1			  2011-07-22		 Bio::TreeIO::nexus(3)
[top]

List of man pages available for Pidora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net