modify muscle.py interface
modify muscle.py interface

The muscle.py API had been modified, breaking run-pycits.py; these
changes restore functionality, preserving as much of the new operation
as possible (e.g. aligning a single file, rather than a directory).

Results namedtuple is streamlined, and filename handling is simplified.

widdowquinn/THAPBI-pycits,widdowquinn/THAPBI-pycits