To separating fragments with identical length via changing in secondary structure
I'd rather say to separate DNA fragments according to size without interfering possible secondary structures (which might lead to changes in running speed so that DNA with same size but different secondary structure might be not separated). Denatured DNA is also single-stranded with some positive effect.
Altogether denaturation reduces effects of DNA structures and increases resolution.
And I guess Ali meant DGGE.
AFLP could be analyzed on polymers using Genetic analyzers (capillary electrophoresis) and not only denaturing polyacrylamide gel.
both of the techniques are used because AFLP is highly informative and it detects length differences down to one single base. Those techniques has a high resolution separation power down 1 single base and the gel can be wide up to 60 cm and its length and the capillary length could reach 80 cm which give support to resolve all the fragments clearly and can compare many samples in the same time.
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