Does anybody have idea to determine polymorphic bands in a binary matrix (ISSR) and how to calculate the genotypes provided from each locus. I calculated the number of bands which present 0 and 1 in the different isolates and I divided it by the total of bands (I considered the bands that gave 1 for all isolates as monomorphic band) I found 80 % of polymorphism however when I constructed the dendrogramme (BY UPGMA) it show a very similar structure for the majority of isolates with low variability and low valor of boostrap. I can't see the logic of this result. ..Thank you for your help.
I don't know if you correctly determined polymorphism. anyway, If this may be due to ISSR couldn't find similarity among, so It will be required another technique for differentiating between isolates or used more primers.
Good Luck!
Dear Safa,
To calculate genetic diversity parameters (number of polymorphic loci, among others), you can use AFLPsurf or GeneAlex softwares for example.
Katarzyna
Ms. Safa,
Use Popgene, TFPGA and/or GenALEx software packages for those analyses. Make sure the parameters used for all the cases should be equal to get the exact results from different packages.
https://sites.ualberta.ca/~fyeh/popgene.html
http://biology-assets.anu.edu.au/GenAlEx/Welcome.html
http://www.marksgeneticsoftware.net/tfpga.htm
Hi,
For dominant markers like ISSR, you can determine many genetic diversity parameters like Nei gene diversity, Shanon information index, effective No. of alleles, etc. Please read the paper attached and other papers published by our team.
You van use Genalex and Popgun for such analyses.
Regards
Masoud Sheidai
Hi
Can you put the preparation data format in excel sheet here which you used for GenAlex analysis. Thank you
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