Dear Karine Durand ,

you can convert from fasta to ms format in DNAsp: http://www.ub.edu/dnasp/ or in fastaconvtr: https://github.com/CRAGENOMICA/fastaconvtr. If you have several populations you can estimate within and between population summary statistics with msSS.pl, a script from Naoki Takebaiashi: https://1drv.ms/u/s!An30RV_2QfTig5ALb9OQf4Dt0wenrQ.

Hope this can help you,

Let me know if you have any problem with any of those scripts.

Best,

https://www.jstor.org/stable/41674639?seq=1#page_scan_tab_contents

This may help you.

Thanks to all of you for the quick response to my questions

I will quickly try the tools and give you a feedback

Hello just a quick update, i have convert from fasta to ms with fastaconvtr whitch is quite nice.

I have a last problem for the moment the summary statistic (theta for example) are not the same if i calculate with EGGLIB on my fasta file and with mscalc on my ms file for the same file.

Is anyone have an idea?

Best,

Dear Karine Durand ,

it is hard to tell why the results are different without more information about your data and about the values of Watterson's Theta you are obtaining. My guess is that the results might be different because mscalc is considering only your segregating sites (as it uses ms' input), while egglib is considering the whole sequences.

If you can give more details on your files and the results you got I might be more helpful.

Best,