2to3 crashes with a apparently simple for.
An example is presented (the first line is actually enough)

        >>> for clade in tree.find_clades(branch_length=True, order='level'):
        >>>     if (clade.branch_length < .5 and
        >>>         not clade.is_terminal() and
        >>>         clade is not self.root):
        >>>         tree.collapse(clade)

The stack is shown below. It almost seems a problem with newline conversion at the end?

RefactoringTool: Can't parse docstring in xx2 line 1: ParseError: bad input: type=0, value='', context=('', (2, 0))
RefactoringTool: Can't parse docstring in xx2 line 2: ParseError: bad input: type=5, value='    ', context=('\n', (2, 0))
RefactoringTool: Can't parse docstring in xx2 line 3: ParseError: bad input: type=5, value='        ', context=('\n\n', (3, 0))
RefactoringTool: Can't parse docstring in xx2 line 4: ParseError: bad input: type=5, value='        ', context=('\n\n\n', (4, 0))
RefactoringTool: Can't parse docstring in xx2 line 5: ParseError: bad input: type=5, value='        ', context=('\n\n\n\n', (5, 0))
RefactoringTool: No files need to be modified.

You are supposed to use “...” on continuation lines, not “>>>”:
http://docs.python.org/glossary#term-1
http://docs.python.org/dev/library/doctest#how-are-docstring-examples-recognized

Please reopen it the problem persists after this change. Thank you!