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Man Pages


Manual Reference Pages  -  BIO::TREEIO::CLUSTER (3)

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NAME

Bio::TreeIO::cluster - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output

CONTENTS

SYNOPSIS



  # do not use this module directly
  use Bio::TreeIO;
  use Algorithm::Cluster;
  my ($result, $linkdist) = Algorithm::Cluster::treecluster(
    distances => $matrix
  );
  my $treeio = Bio::TreeIO->new(
    -format   => cluster,
    -result   =>  $result,
    -linkdist =>  $linkdist,
    -labels   =>  $labels
  );
  my $tree = $treeio->next_tree;



DESCRIPTION

This is a driver module for parsing Algorithm::Cluster::treecluster() output.

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 - Guillaume Rousse

Email Guillaume-dot-Rousse-at-inria-dot-fr

CONTRIBUTORS

Jason Stajich - jason-at-bioperl-dot-org

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::cluster->new();
 Function: Builds a new Bio::TreeIO::cluster object for reading Algorithm::Cluster::treecluster output
 Returns : Bio::TreeIO::cluster
 Args    :-result   => Algorithm::Cluster result
          -linkdist => distance between links
          -labels   => node labels



    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   :
 Function: Sorry not possible with this format
 Returns : none
 Args    : none



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perl v5.20.3 BIO::TREEIO::CLUSTER (3) 2016-04-05

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