Batch pairwise alignment and consensus

Question

[lewis272727]

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.

[Joe]

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?

[lewis272727]

Yeah, I guess you could call it the conserved regions? All the bases which are identical once the sequences are aligned.

[WouterDeCoster]

Why do you think this would be a good approach?

Answer 1

[Michael]

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.

[lewis272727]

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.

[GenoMax]

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.