def phylogeneticTreeFromFile(self, treefile, file_format):
dataset = Dataset()
dataset.read(open(treefile, 'rU'), schema=file_format)
dendropy_tree = dataset.tree_lists[0][0]
tree = PhylogeneticTree(dendropy_tree)
tree.calc_splits()
delete_outdegree_one(tree._tree)
return tree
def read_tree_from_file(self, treefile, file_format):
dataset = Dataset()
dataset.read(open(treefile, 'rU'), schema=file_format)
dendropy_tree = dataset.trees_blocks[0][0]
self._tree = dendropy_tree
self.n_leaves = self.count_leaves()