You actually don't need to mess with `PYTHONPATH` when using `pip install -e .`. This method of installation is useful when you're going to develop/contribute to scikit-bio, as links are created in the site-packages directory (e.g., of the current virtualenv). This way, when you make changes to a source code file, you don't have to rerun `python setup.py install` in order to have those changes take effect.

I recommend keeping this command (with an explanation of what it does), noting that this is useful for those intending to develop scikit-bio. You might also include the `python setup.py build_ext --inplace` command as an alternative (in case users want to set `PYTHONPATH` instead of installing to a virtualenv or something, either to develop or use the software).