Merge remote-tracking branch 'upstream/master'
updated 12-7
Generalized file extension outputs, fixed method redundancy, and added AlignIO input validation
Example Input Tree File
Specified Biopython v1.6
Updated -h descriptions.
Merge remote-tracking branch 'upstream/master'

Conflicts:
	HYPNO.py
Fixed FASTA formatting
Fixed non-ASCII characters
Merge pull request #12 from nemami/master

Request 1/7