Mutations in sequences relative to reference (histogram)
You can use AlignBuddy to process alignments in GenBank format, which allows you to keep the metadata. From the command line:

$: alignbuddy input.gb --generate_alignment mafft | \
   alignbuddy --extract_feature_sequences 'PROT_FEAT_1' | \
   alignbuddy --percent_id


If you want to do a large one-to-many comparison and loop through a bunch of features, I'd recommend importing AlignBuddy into a custom python script and calling the relevant functions directly. You can then collect the relevant data and build a histogram with matplotlib.