Hi Chandima! Hope you are well, you can use Grunwald tutorial https://grunwaldlab.github.io/Population_Genetics_in_R/Linkage_disequilibrium.html

Is in R environment and it uses association index. Also Fstat sotware is older but still accepted. Good luck with your research

Cheers

One commonly used tool for estimating linkage disequilibrium in haploid organisms like fungi is PLINK. PLINK is a whole-genome association analysis toolset that provides a variety of functions for analyzing genetic data, including calculating linkage disequilibrium.

To estimate linkage disequilibrium in haploid fungi using PLINK, you would typically need to have genotype data for a set of genetic markers (e.g., SNPs) from your fungal samples. You can then use PLINK to calculate measures of linkage disequilibrium, such as r-squared values, between pairs of markers in your data set.

Another tool that is commonly used for estimating linkage disequilibrium in fungi and other haploid organisms is Haploview. Haploview is a software package that provides various functions for analyzing genetic variation, including calculating linkage disequilibrium and creating LD plots.

Both PLINK and Haploview are widely used and well-documented tools that can be useful for estimating linkage disequilibrium in haploid organisms like fungi. You can find more information about these tools and download them from their respective websites.

Dear Ignacio and David

Thank you so much for introducing those wonderful tools. I tried those and some other tools also and got comparable estimates.

Regards

Chandima