NAME

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

SYNOPSIS

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

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:

  http://bugzilla.open-bio.org/

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 = new Bio::TreeIO::cluster();
 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