create alignment submodule

~~**NOT READY FOR MERGE**  Working on some doc issues, but I want travis to run the tests in the meantime.~~

Doc issues sorted out, I think this should be ready to go, but we need to remember to test install/testing with setup.py before the release since I did have to make changes to setup.py. 

Fixes #419.

These are in ``alignment/__init__.py``, so we'd be able to import as:

```
from skbio.core.alignment import StripedSmithWaterman, AlignmentStructure, align_striped_smith_waterman
```
and soon (#) they'll also be in ``skbio/__init__.py``, so you could import as:

```
from skbio import StripedSmithWaterman, AlignmentStructure, align_striped_smith_waterman
```

I say we leave as-is for now - don't want to create confusion by having them importable from a 3rd location. Sound ok? We can always re-visit later.