I am analyzing rDNA sequences from organisms in different countries. One of the locations seems to be very different from the other ones, and when aligning there are blocks of gaps. When I analyze these sequences without gap trimming in Arlequin or GenAIEx I have a lot of noise. Therefore, I was thinking that perhaps removing these gaps would give me better and more reliable results. Does someone have experience with this? Which is the normal threshold from trimming?
Suzana Radojkovic
Noise happens to everybody from time to time. I would try to purify DNA and repeat PCR for sequencing and sequencing.
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