Provided by: libbio-perl-perl_1.7.6-3_all bug

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://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)