To see if this has an impact, you can do this: d0 <- dist.dna(x, "N") d1 <- dist.dna(x, "N", pairwise.deletion = TRUE) plot(d0, d1) abline(0, 1, lty = 3) # draw x = y line
Best, Emmanuel ----- Le 6 Mai 20, à 21:35, Marc Domènech Andreu <mdome...@gmail.com> a écrit : > Oh ok thanks. Well my sequences are COI sequences, a mitochondrial protein > coding gene so there are no gaps in the middle. However, there are in the > extremes, some sequences being longer than others. So I will set > pairwise.deletion=TRUE as you suggest. > Thanks, > Marc > On Tue, May 5, 2020 at 5:03 AM Emmanuel Paradis < [ > mailto:emmanuel.para...@ird.fr | emmanuel.para...@ird.fr ] > wrote: >> ----- Le 5 Mai 20, à 0:36, Marc Domènech Andreu < [ >> mailto:mdome...@gmail.com | >> mdome...@gmail.com ] > a écrit : >>> Hi, >>> Yes I tried it. Most of the results are very similar but some change. Do you >>> know the difference between those two methods? >> model = "N" is the Hamming distance (absolute number of differences between >> two >> sequences) >> model = "raw" is the Hamming distance divided by the sequence length (aka >> uncorrected distance, or p-distance) >> About the use of 'pairwise.deletion' in dist.dna(): in fact there is no >> simple/unique solution for this option. It depends very much on the data at >> hand and the distribution of "missing data", especially gaps. You need to >> check >> their distribution, for example with image(x) of image(x, what = "-") where >> 'x' >> is the DNA data. You may get nonsensical results leaving the default >> pairwise.deletion = FALSE if there are long gaps. Even a small number of gaps >> may be problematic if there are in a column (site) which is polymorphic. >> Best, >> Emmanuel >>> Thanks, >>> Marc >>> On Mon, May 4, 2020 at 2:44 PM Emmanuel Paradis < [ >>> mailto:emmanuel.para...@ird.fr | emmanuel.para...@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 [ >>>> mailto:mdome...@gmail.com | >>>> 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 < [ >>>>> mailto:zkam...@gmail.com | >>>> > 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 >>>> >> [ mailto:R-sig-genetics@r-project.org | R-sig-genetics@r-project.org ] >>>>>> [ https://stat.ethz.ch/mailman/listinfo/r-sig-genetics | >>>> >> 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 >>>> > [ mailto:R-sig-genetics@r-project.org | R-sig-genetics@r-project.org ] >>>>> [ https://stat.ethz.ch/mailman/listinfo/r-sig-genetics | >>>> > 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. > -- > Marc Domènech Andreu > PhD student at University of Barcelona. > Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals. 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