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

[Marc Domènech Andreu]

Hi,
Yes I tried it. Most of the results are very similar but some change. Do
you know the difference between those two methods?
Thanks,
Marc

On Mon, May 4, 2020 at 2:44 PM Emmanuel Paradis <emmanuel.paradis using ird.fr>
wrote:

> Hi Marc,
>
> Have you tried model = "N" in dist.dna()?
>
> Best,
>
> Emmanuel
>
> ----- Le 4 Mai 20, à 16:44, Marc Domènech Andreu mdomenan using gmail.com a
> écrit :
>
> > Thanks for your answer. For computing the distance matrix I am using the
> > dist.dna function in Ape package, with the model set to "raw"
> > and pairwise.deletion = FALSE. However I don't know exactly the equation
> or
> > formula pegas uses for AMOVA.
> > I am working with a mitochondrial marker so it would be haploid.
> > Marc
> >
> > On Wed, Apr 29, 2020 at 5:26 PM Zhian N. Kamvar <zkamvar using gmail.com>
> wrote:
> >
> >> 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
> >> >
> >>
> >> _______________________________________________
> >> R-sig-genetics mailing list
> >> R-sig-genetics using r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
> >>
> >
> >
> > --
> > *Marc Domènech Andreu*
> > PhD student at University of Barcelona.
> > Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals.
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-genetics mailing list
> > R-sig-genetics using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
>


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

	[[alternative HTML version deleted]]