repeat.py, repeat_score.py: use parameters from configobj to identify ambiguous parameters. Clearly distinguish the true msa (msa) from an altered msa with standard AAs only (msa_standard_aa)
hmm_viterbi.py: Get info on ambiguous chars from congifobj configurations file
defaults.ini: Add (ambiguous) AAs
sequence.py: Save original sequence, and sequence with standard AAs only
Mark slow test functions with pytest.mark.slow