Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
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 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

   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 v5.32.1			  2019-12-07		 Bio::TreeIO::nexus(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::TreeIO::nexus&sektion=3&manpath=FreeBSD+13.0-RELEASE+and+Ports>

home | help