Hi August,

First of all, you have to have sure that your alignment is the same in both softwares (please, check if you have no differences between what you see in MEGA and what you got in DNAsp). The number of segregating sites (S) is merely a counting measure so it should be the same. Several metrics (if not all of them) are based on S, since S is different so the other metrics.

A simple test is to load the same fasta file you exported in both softwares, instead only in the DNAsp, if you are losing some info through the conversion process you should notice that.

Also, please, pay attention whether you are picking up some option through DNAsp importing process that could reduce your data se somehow, as defining taxa sets or sequences sets or regions.

Regarding to have the metrics for each species, It is entirely up to you. If such information for each species will help you in your hypothesis test, then yes, you should go forward. Otherwise, you be fine with the dataset overview. Nonetheless, since each species is obviously independent evolutionary unities, Tajima's D might behavior differently for each species. Therefore, In my opinion, you should take it independently as well.

I assume you're doing some species delimitation analysis with COI, if you have any question about it, don't be afraid to text me.

Cheers

Thank you so much for your detailed answer Wilson Frantine-Silva! I will se if i cant figure it out based on what you have told me.

Hi August

Can you send me a link for DnaSP software for downloading? I searched it more but I cannot find an available site for downloading or using online. I am sorry for this inconvenience.

Ahmed Elfadadny You can download it from the following link http://www.ub.edu/dnasp/

you can use this paper as a referance

https://academic.oup.com/bioinformatics/article/25/11/1451/332507

Best of luck

Hend Altaib Thank you very much

All the best