removes dependence on cogent's DNA, LoadSeqs, Alignment, DenseAlignment

~~**NOT READY FOR MERGE**~~

``$ gc "from cogent.*Alignment" qiime scripts tests``
~~qiime/filter_alignment.py:14:from cogent.core.alignment import DenseAlignment~~ #1500
- [x] qiime/util.py:55:from cogent.core.alignment import Alignment
~~scripts/insert_seqs_into_tree.py:18:from cogent.core.alignment import DenseAlignment~~ #1499 
- [x] tests/test_align_seqs.py:19:from cogent.core.alignment import DenseAlignment, Alignment

``$ gc "from cogent.*LoadSeqs" qiime scripts tests``
- [x] qiime/make_phylogeny.py:21:from cogent import LoadSeqs, DNA
- [x] qiime/pick_otus.py:27:from cogent import LoadSeqs, DNA
~~qiime/split_libraries.py:49:from cogent import DNA as DNA_cogent, LoadSeqs~~ #1501
- [x] qiime/util.py:52:from cogent import LoadSeqs, Sequence
- [x] scripts/filter_otus_by_sample.py:19:from cogent import LoadSeqs
- [x] tests/test_align_seqs.py:18:from cogent import LoadSeqs, DNA
- [x] tests/test_assign_taxonomy.py:25:from cogent import LoadSeqs
~~tests/test_filter_alignment.py:15:from cogent import LoadSeqs~~ #1500
- [x] tests/test_filter_otus_by_sample.py:17:from cogent import LoadSeqs
- [x] tests/test_identify_chimeric_seqs.py:18:from cogent import LoadSeqs, DNA
- [x] tests/test_make_phylogeny.py:18:from cogent import LoadSeqs, DNA
- [x] tests/test_parallel/test_assign_taxonomy.py:18:from cogent import LoadSeqs
- [x] tests/test_parallel/test_blast.py:17:from cogent import LoadSeqs
- [x] tests/test_parallel/test_identify_chimeric_seqs.py:17:from cogent import LoadSeqs
- [x] tests/test_parallel/test_util.py:18:from cogent import LoadSeqs
- [x] tests/test_pick_rep_set.py:17:from cogent import LoadSeqs
- [x] tests/test_split.py:17:from cogent import LoadSeqs
- [x] tests/test_workflow/test_pick_open_reference_otus.py:19:from cogent import LoadTree, LoadSeqs
- [x] tests/test_workflow/test_upstream.py:18:from cogent import LoadTree, LoadSeqs

``$ gc "from cogent.*DNA" qiime scripts tests``
- [x] qiime/align_seqs.py:33:from cogent import DNA as DNA_cogent
~~qiime/filter_alignment.py:13:from cogent import DNA~~ #1500
- [x] qiime/make_phylogeny.py:21:from cogent import LoadSeqs, DNA
- [x] qiime/pick_otus.py:27:from cogent import LoadSeqs, DNA
~~qiime/split_libraries.py:49:from cogent import DNA as DNA_cogent, LoadSeqs~~ #1501
- [x] scripts/insert_seqs_into_tree.py:19:from cogent.core.moltype import DNA
- [x] scripts/insert_seqs_into_tree.py:28:from cogent.core.moltype import DNA
- [x] tests/test_align_seqs.py:18:from cogent import LoadSeqs, DNA
- [x] tests/test_identify_chimeric_seqs.py:18:from cogent import LoadSeqs, DNA
- [x] tests/test_make_phylogeny.py:18:from cogent import LoadSeqs, DNA