4 months ago by
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.