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.paradis at ird.fr | emmanuel.paradis at ird.fr ] > wrote:
----- Le 5 Mai 20, ? 0:36, Marc Dom?nech Andreu < [ mailto:mdomenan at gmail.com |
mdomenan at gmail.com ] > a ?crit :
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.
On Mon, May 4, 2020 at 2:44 PM Emmanuel Paradis < [
mailto:emmanuel.paradis at ird.fr | emmanuel.paradis at ird.fr ] > wrote:
Have you tried model = "N" in dist.dna()?
----- Le 4 Mai 20, ? 16:44, Marc Dom?nech Andreu [ mailto:mdomenan at gmail.com |
mdomenan at gmail.com ] a ?crit :
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:zkamvar at gmail.com |
zkamvar at 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.
On 4/29/20 3:04 AM, Marc Dom?nech 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
for performing AMOVA? I only get to obtain almost identical results when
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
I have too few sequences for those species?
Thanks in advance,
Marc