cleaned up caretta API

bin/caretta-app

bin/caretta-app-demo

bin/caretta-cli

caretta/caretta_utility.py

caretta/dynamic_time_warping.py

caretta/feature_extraction.py

caretta/helper.py

caretta/msa_numba.py

caretta/multiple_alignment.py

caretta/neighbor_joining.py

caretta/pfam.py

caretta/psa_numba.py

caretta/score_functions.py

caretta/superposition_functions.py

setup.py