Other than Arlequin, is there any software or online server recommended to do AMOVA analysis?

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Bonaventure Aman Omondi

What kind of markers are you using? You could do AMOVA on GenAlex, a free Excel Add-in that you will find here: http://biology.anu.edu.au/GenAlEx/Welcome.html

It is fairly easy to install and to learn and to run, but first take the to look at the associated publications.

Good Luck!

Brent Chiazzari

Bonaventure is right on the money! Genalex is fairly easy to use (it is a macro to the program excel). I, HWE, Phi(pt/rt etc.), F(is/it/rt etc.), mantel test, Nei, Nm and more. It can analyse haplotypic, binary, genotypic and other data types too. There are limits and assumptions that affect some of these tests, however.