Bio::TreeIO::cluster(3User Contributed Perl DocumentatiBio::TreeIO::cluster(3)NAMEBio::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:
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 = 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
perl v5.14.1 2011-07-22 Bio::TreeIO::cluster(3)
