Multiple Sequence Alignment between population

Question

[Mannu]

Hello,

I have nucleotide sequence data from different populations. I would like to align them to check SNPs among population. I am wondering about which method will provide me better result

Putting all the sequences in single FASTA file and align them or alignment of individual population followed by alignment of already aligned sequences. Is it worth to follow the second method? What are the tools available for this?

Thanks in advance.

Regards

Answer 1

[Brice Sarver]

They ought to produce the same result unless you have regions that are extremely difficult to align. If it is hard, I'd try the second case first to see if that alleviates the issue. If it doesn't and you aren't confident in your results, you can exclude those sites from analysis.

The standard suite of tools will work: MUSCLE, MAFFT, MACSE for translation alignments, etc.