I am starting a new project with DNA barcoding and I am not sure how to codify sequence DNA. In this project we are using the following molecular markers: rps16-trnk, rpl32-trnl and trnl-trnf (chloroplast).
When I asked this question maybe I was not so clear. I was referring to the correct way of dealing with the DNA sequence to identify barcode. For example, how to deal with insertions, deletions, duplicated regions and microsatellites.