Hey, I have a few hundred forward and reverse reads, and I'd like to align them pair-by-pair and find the consensus of the alignment. Does anyone know of a way to do this? Even if someone knows how to do a batch pairwise alignment without the consensus that would be helpful.
The sequences are in FASTA format, I have already reverse complemented the reverse reads, so I just need something to go through them all and align two sequences at a time (with the end goal being a phylogenetic tree).
Thanks.
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lewis272727 •
You might want to do a multiple sequence alignment instead (MSA). Try Jalview as a starter, or MAFFT maybe should be able to handle 100+ nucleotide seqs.
But that will align all the sequences against each other right? I just want to align the forward and reverse to each other, 2 sequences at a time.
If they are going to align like that then what you are looking to do is to merge them into a longer representation, correct? I recommend bbmerge from BBMap suite.
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The consensus of a pairwise alignment isn’t possible/meaningful... how can you choose between one base or the other? Or are you just after all the sites which are identical?
Can you please elaborate the purpose?
Yeah, I guess you could call it the conserved regions? All the bases which are identical once the sequences are aligned.
Why do you think this would be a good approach?