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Bio::Factory::TreeFactoryI(3pm) User Contributed Perl Documentation Bio::Factory::TreeFactoryI(3pm)


Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees
from/to a data stream


  # get a $factory from somewhere Bio::TreeIO likely
  my $treeio = Bio::TreeIO->new(-format => 'newick', #this is phylip/newick format
                               -file   => 'file.tre');
  my $treeout = Bio::TreeIO->new(-format => 'nexus',
                                -file   => ">");
  # convert tree formats from newick/phylip to nexus
  while(my $tree = $treeio->next_tree) {


This interface describes the minimal functions needed to get and write trees from a data stream. It is implemented by the Bio::TreeIO factory.


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Please direct usage questions or support issues to the mailing list:

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.

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AUTHOR - Jason Stajich



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : next_tree
 Usage   : my $tree = $factory->next_tree;
 Function: Get a tree from the factory
 Returns : L<Bio::Tree::TreeI>
 Args    : none


 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Writes a tree onto the stream
 Returns : none
 Args    : L<Bio::Tree::TreeI>
2021-08-15 perl v5.32.1