Reference

Bio::TreeIO::lintree(3pm)

Parser for lintree output trees

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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-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)

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