function OUT_DATA=CalculateProteinEntropy(Ref, ALIGN_CELL)

OUT_DATA = cell(size(ALIGN_CELL));
for i = 1:size(ALIGN_CELL,1)
    
    aligned_seqs = ALIGN_CELL{i};
    
    ref_seq = Ref.Sequence;
    
    ref_prof = seqprofile(ref_seq, 'alphabet', 'aa');
    seqs_prof = seqprofile(aligned_seqs, 'alphabet', 'aa');
    
    [mp, H1, H2] = profalign(ref_prof, seqs_prof);
    
    merged_seqs = char(zeros(size(aligned_seqs,1)+1, size(mp,2)));
    merged_seqs(2:end, H2) = aligned_seqs;
    merged_seqs(1, H1) = ref_seq;
    
    entropy_vals = CalculateEntropy(merged_seqs);
    
    %only pull out the values that are in the reference positions
    ref_entropy = entropy_vals(H1);
    
    OUT_DATA{i} = ref_entropy;
end