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.
Question: Using a Multiple Seq Alignment tool for pairwise alignments possible?
3.1 years ago by
nchuang • 200
nchuang • 200 wrote:
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