Bio::TreeIO::lintree(3pm)				User Contributed Perl Documentation				 Bio::TreeIO::lintree(3pm)

NAME

       Bio::TreeIO::lintree - Parser for lintree output trees

SYNOPSIS

	 # do not use directly, use through Bio::TreeIO
	 use Bio::TreeIO;
	 my $treeio = Bio::TreeIO->new(-format => 'lintree',
				      -file   => 't/data/crab.nj');
	 my $tree = $treeio->next_tree;

DESCRIPTION

       Parser for the lintree output which looks like this

	 13 sequences	  1000 bootstraping
       1 A-salina
       2 C-vittat
       3 C-sp.
       4 L-aequit
       5 P-camtsc
       6 E-tenuim
       7 L-splend
       8 P-bernha
       9 P-acadia
       10 P-p(NE)
       11 P-p(GU)
       12 P-l(NE)
       13 P-l(GU)
	14 and	 2	  0.098857	1000
	14 and	 3	  0.127932	1000
	15 and	 1	  0.197471	1000
	15 and	14	  0.029273	 874
	16 and	10	  0.011732	1000
	16 and	11	  0.004529	1000
	17 and	12	  0.002258	1000
	17 and	13	  0.000428	1000
	18 and	16	  0.017512	1000
	18 and	17	  0.010824	 998
	19 and	 4	  0.006534	1000
	19 and	 5	  0.006992	1000
	20 and	15	  0.070461	1000
	20 and	18	  0.030579	 998
	21 and	 8	  0.003339	1000
	21 and	 9	  0.002042	1000
	22 and	 6	  0.011142	1000
	22 and	21	  0.010693	 983
	23 and	20	  0.020714	 996
	23 and	19	  0.020350	1000
	24 and	23	  0.008665	 826
	24 and	22	  0.013457	 972
	24 and	 7	  0.025598	1000

       See http://www.bio.psu.edu/People/Faculty/Nei/Lab/software.htm for access to the program and N Takezaki, A Rzhetsky, and M Nei,
       "Phylogenetic test of the molecular clock and linearized trees." Mol Biol Evol 12(5):823-33.

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-bioperl-dot-org

CONTRIBUTORS

       Ideas and discussion from:
	Alan Christoffels
	Avril Coghlan

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::TreeIO::lintree->new();
	Function: Builds a new Bio::TreeIO::lintree object
	Returns : an instance of Bio::TreeIO::lintree
	Args	: -nodetype => Node type to create [default Bio::Tree::Node]

   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

   nodetype
	Title	: nodetype
	Usage	: $obj->nodetype($newval)
	Function:
	Example :
	Returns : value of nodetype (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

perl v5.14.2							    2012-03-02						 Bio::TreeIO::lintree(3pm)