def main(self, taxonomy, output_tree, output_tax, no_unique_tax,<EOL>decorate, seqinfo):
<EOL>if self.reference_tree:<EOL><INDENT>self._reroot()<EOL><DEDENT>td =  TreeDecorator(self.tree,<EOL>taxonomy,<EOL>seqinfo)<EOL>if decorate:<EOL><INDENT>td.decorate(output_tree, output_tax, no_unique_tax)<EOL><DEDENT>else:<EOL><INDENT>logging.info("<STR_LIT>" % (output_tree))<EOL>self.tree.write(<EOL>output_tree,<EOL>format = "<STR_LIT>"   <EOL>)<EOL><DEDENT>
Decorate and if necessary, re-root the tree. If an old reference tree
        is provided it is assumed that re-rooting is desired

        Parameters
        ----------
        taxonomy: str
            Path to a GreenGenes formatted, or taxtastic formatted taxonomy 
            file, containing the taxonomy of all or some if the sequences used 
            to construct the tree. This taxonomy will be used by the 
            tree_decorator.TreeDecorator class to decorate self.tree
        output_tree: str
            Path to file to which the decorated tree will be written to.
        output_tax: str
            Path to file to which the decorated taxonomy will be written to.
        seqinfo: str
            path to taxtastic seqinfo file to be used with taxonomy to annotate
            the tree.