Add a class for MSA

[Donaim]

Compared to CIGAR, the MSA format contains the actual values for nucleotides in the aligned sequences.
For this, MSA is commonly used for tracking mutations, for example, for resistance interpretations.

Let's create an MSA class for objects that will make this, and other common operations easier.

One challenge will be that MSA is often represented as tuples of strings. In existing aligntools code, too.
Not sure how to both maintain backwards compatibility and not complicate the representation of MSA objects.