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 = new Bio::TreeIO(-format => 'newick', #this is phylip/newick format -file => 'file.tre'); my $treeout = new Bio::TreeIO(-format => 'nexus', -file => ">file.nexus"); # convert tree formats from newick/phylip to nexus while(my $tree = $treeio->next_tree) { $treeout->write_tree($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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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>
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.