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

[Zhian N. Kamvar]

This highly depends on the distance function you are using for pegas:

1. How does it treat missing data? I believe Arlequin treats missing 
data by dropping them from the denominator.

2. If you have a diploid species, does it calculate distance for haplotypes?

Both of these can affect the resulting Phi values. You might also try 
poppr.amova() with the method = "pegas" function to automate the process.

Best,

Zhian

On 4/29/20 3:04 AM, Marc Domènech Andreu wrote:
> 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
>