Added branch length recalculation and subtree midpoint rooting.
Filter out protein sequences that lack nucleotide sequence.
Merge pull request #10 from nemami/master

Complete Genetic Code implementation, including mitochondrial sequences
Updated README usage and outputs
Commented out nearest neighbor alignment to enable usage when --tree is not specified.
Cleaned up debugging code consisting of print statements.
Added ability to run HYPNO without the --tree option in case user wants to only retrieve and align nucleotide sequences. Also added code for merging subtree alignments into a single output MSA.
Merge branch 'master' of github.com:mazimi/HYPNO
Merge remote-tracking branch 'upstream/master'

Conflicts:
	HYPNO.py