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;
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