ENH: read_newick
ENH: added sniffer, writer, and docs
Merge branch 'master' of https://github.com/biocore/scikit-bio

Conflicts:
	skbio/io/__init__.py
	skbio/io/_exception.py
Initial port of Alignment phylip writer and tests

Writer now streams data to file; minor cleanup to code and tests, stil more to do.
Refactor error-case unit tests to remove duplication
Update phylip writer to use Alignment.is_valid

No longer breaks encapsulation. Also updated error messages to better match I/O framework.
Phylip writer checks ID length <= 10 chars.
Phylip writer now raises PhylipFormatError

Instead of SequenceCollectionError. Makes more sense in the context of I/O.
Phylip writer outputs fixed-width first column

Padded to 10 chars.
updated TreeNode and deprecated to_newick, from_newick, from_file
Phylip writer now split sequences into blocks
TST: fixed python3 in test_newick.py
TST: py3 - this better work...
TST: py3 - float() argument must be a string or a number, not 'NoneType'
TST: python lambdas are unhelpful
Add BiologicalSequence.update

Still needs unit tests.
MAINT: improved sniffer readability
MAINT: minor changes
BiologicalSequence.update -> BiologicalSequence.copy

After discussion with @ebolyen, we decided that copy is a better name for the method. It now accepts **kwargs instead of a dict, simplifying the implementation and API.

Still need to add unit tests.
add tests for BiologicalSequence.copy