Question: Multiple Sequence Alignment between population
gravatar for Mannu
5.6 years ago by
United States
Mannu0 wrote:


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.


alignment • 1.2k views
ADD COMMENTlink modified 5.3 years ago by Biostar ♦♦ 20 • written 5.6 years ago by Mannu0
gravatar for Brice Sarver
5.6 years ago by
Brice Sarver3.5k
United States
Brice Sarver3.5k wrote:

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.

ADD COMMENTlink written 5.6 years ago by Brice Sarver3.5k
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