biocore/qiime — pull request #1503 by gregcaporaso (2014-04-11 02:43:50+00:00)
Title: removes dependence on cogent's Sequence object

there are still dependencies in the denoiser code, which is going to go away, and in filter_alignment.py, which is being rewritten (#1500).

**NOT READY FOR MERGE**: this contains commits from #1497, so that should be merged first, and then I'll merge that into this.