mean Tajima's D value

Question

[biosol]

Hi all,

I have calculated Tajima's D value for several windows in my data. Some of those windows contain just 1 or 2 SNPs, so I would like to combine their Tajima's D value into one (of a bigger region). Is it enough with calculating the mean Tajima's D value of those smaller regions or is there something else I should take into account?

Thanks in advance guys :)

Answer 1

[pltbiotech_tkarthi]

Hello, First of all I don't know which software you have used. If you use, DNAsP, there is a sliding window option to calculate, you could adjust the windows length and size and it will calculate region by region. If not, you don't need to click the sliding window option in DNAsP, the program will automatically calculate the Tajima D value of the whole region of the multiple alignment input file (fasta) or the fragments of multiple alignment input file (fasta). But in any case you have to choose, whether you would like to calculate from the total number of mutations or only from segregating sites.

Also, you could try with MEGA (Molecular Evolutionary Genetics Analysis) software to calculate the Tajima D value of whole region of the multiple alignment input file (fasta). Hope this suggestion may help.