Replace pairwise2 with PairwiseAligner

[Ulthran]

No description provided.

[Ulthran]

Avoiding the weird alignment parsing seems impossible in the new Biopython. To get the sequences with dashes you have to call Alignment.format and it then has big complicated functions for iterating over the alignment and displaying it but it never exposes the exact strings we want. Checkout format_pretty and the clustal format_alignment for reference.

[kylebittinger]

You should be able to use __getitem__ to access the aligned sequences. For example, if a is an alignment object, then a[0] and a[1] should give the aligned sequences as strings. See here in the docs for the Alignment class.