I used the ISSR tehniques. From the beginning I isolated the DNA and I amplified the DNA using ISSR primers (7 primers- inter simple sequence repeat markers-ISSR). I obtained 7 agarose electrophoresis gels each having different numbers of band for each individuals from plant population. How can I determine the genetic diversity using Nei index(or Shanon). What soft (for free) is suitable for analyse the 7 electrophoretic gels and to corroborate the results for all individuals from population?
Hopping to receive an answer, thank you very much,
Carmen
POPGENE version 1.31, use this software and GenAlex
just google it and you can freely download these software with user manual
Hi Carmen,
First of all try to score all the bands visible on the gel in a binary matrix.
For each and present score 1 and absent band score 0 for each plant. Combine the data i.e. present or absent bands in a matrix form.
Then feed the data in the software (For a free one try POPGENE). You will get many parameters of your choice.
Hello! Thank you very much. I will try to see if I obtained a good result.
Have a nice day!
You can analyze the prepared matrix using number of software, depending on which parameters you need:
POPGENE Software for Population Genetic Analysis (Allele Frequency, Allele Number, Effective Allele Number, Polymorphic Loci, Obs. Homozygosity, Exp. Homozygosity, Shannon Index, Gene Diversity, Homogeneity Test:, F-Statistics, Gene Flow, Genetic Distance, Dendrogram
GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. http://biology.anu.edu.au/GenAlEx.
Arlequin http://cmpg.unibe.ch/software/arlequin3
STRUCTURE Pritchard et al. 2000 infer population structure and assign individuals to populations https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461096/pdf/10835412.pdf
DARwin is a software package developed for diversity and phylogenetic analysis on the basis of evolutionary dissimilarities
http://darwin.cirad.fr/
Hi,
At first you score the bands and generate binary matrix data, presence of band for 1 and absence of the respective band is 0. You have to score minimum 100 bands, which will generate a meaning full data. If your 7 ISSR primer does not generate 100 and above fragments, you may increase the number of primer. Because your are estimating the diversity using minimum 100 loci. After creating binary matrix data, you may use any related software like NTSys, POPGENE.
Hi Carmen Maximilian,
I suggest "Geneticstudio"
https://dyerlab.ces.vcu.edu/tag/software/
- Badges
- Science method