Hi Marc, Have you tried model = "N" in dist.dna()?
Best, Emmanuel ----- Le 4 Mai 20, à 16:44, Marc Domènech Andreu mdome...@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 <zkam...@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@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@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-genetics _______________________________________________ R-sig-genetics mailing list R-sig-genetics@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
