I am using GelCompar II software to analyze and create a presence/absence matrix from ISSRs using nuclear DNA. I have concerns that the software is not coming up with acurate band matching or band calling due to the following issues.
I have 11 different primers, 15 populations and 450 individuals in one project. They are organized on 5 PCR plates, with three populations of 30 individuals plus a negative and positive control for each population. I attached a structure diagram using K=3 (just as an example, not the actual suggested k). The populations are arranged in alphabettical order, and appear to be falling together based on the plate they are on.
The other project i have 488 individuals with 10 primers and 11 populations. These are randomized over 6 plates and the analyses are showing totally random data. (attached)
Does anyone use gelcompar II? Am i missing some sort of setting in the program? does anyone have any ideas? I have increased optimization and tolerance settings and taken out the smallest and largest few bands fo each gel. Any help would be appreciated.