[R-sig-genetics] Pegas vs Arlequin, and negative AMOVA values

[Marc Domènech Andreu]

Hello everyone,
I would like to ask for help with two questions regarding AMOVA and the
Pegas package.
1. Do you know which is the formula or equation that Pegas and Arlequin use
for performing AMOVA? I only get to obtain almost identical results when I
set "is.squared = FALSE" in pegas and "Locus by locus AMOVA" in Arlequin.
2. I'm doing the analyses for several species, and for some of them I
obtained negative AMOVA results. I know slightly negative results are not
uncommon and as far as I know they should be treated as 0, but in some
cases they are very negative, such as -25%. Why can this be? Maybe because
I have too few sequences for those species?
Thanks in advance,
Marc

-- 
*Marc Domènech Andreu*
PhD student at University of Barcelona.
Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals.

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