Quick question. A Multiple Sequence alignment (MSA) uses dynamic programming to create alignments. Would it still be able to give a good global pairwise alignment? I tried it with TCoffee and result looked good for a query sequence with large indel and it was fast. I am just trying to get a collection of sequences aligned to a reference sequence (preferable output in fasta format). I was trying Python Pairwise2 but apparently it can't do large sequences (>3500bases) without being extremely slow.