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YES!
<div class="">that was the bit I was missing, </div>
<div class="">many thanks for help</div>
<div class="">cheers</div>
<div class="">M.</div>
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__________________________________</div>
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<font class="Apple-style-span" color="#004D95"> Massimiliano Virgilio, PhD <br class="">
<br class="">
Royal Museum for Central Africa <br class="">
<br class="">
</font></div>
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<font class="Apple-style-span" color="#004D95">Joint Experimental Molecular Unit (JEMU)</font></div>
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<font class="Apple-style-span" color="#004D95">Leuvensesteenweg 13, B-3080 Tervuren, Belgium, +32 (0) 27695366<br class="">
<br class="">
<a href="mailto:massimiliano.virgilio@africamuseum.be" class="">massimiliano.virgilio@africamuseum.be</a> <br class="">
<br class="">
<a href="http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/" class="">http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/</a></font></div>
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<font class="Apple-style-span" color="#004D95"><a href="http://jemu.myspecies.info" class="">http://jemu.myspecies.info</a></font></div>
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<blockquote type="cite" class="">
<div class="">On 07 Apr 2015, at 16:57, Zhian Kamvar <<a href="mailto:zkamvar@gmail.com" class="">zkamvar@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Actually, about does work on populations if you give it a genpop object.<br class="">
<br class="">
Cheers,<br class="">
Zhian<br class="">
<blockquote type="cite" class="">On Apr 7, 2015, at 07:53 , Virgilio Massimiliano <<a href="mailto:massimiliano.virgilio@africamuseum.be" class="">massimiliano.virgilio@africamuseum.be</a>> wrote:<br class="">
<br class="">
Hi Zhian,<br class="">
<br class="">
many thanks for your answer,<br class="">
<br class="">
The problem with aboot it that it calculates distances among individuals<br class="">
(and I have some 800 individuals) but not among populations.<br class="">
<br class="">
The reason I was using pairwise.fst of adegenet was that it has a pop<br class="">
argument, similarly dist.genpop works with populations.<br class="">
<br class="">
Or do you have a way of using aboot on populations?<br class="">
<br class="">
Cheers <br class="">
<br class="">
M.<br class="">
<br class="">
<br class="">
On 07/04/15 16:10, "Zhian Kamvar" <<a href="mailto:zkamvar@gmail.com" class="">zkamvar@gmail.com</a>> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">Hello,<br class="">
<br class="">
I have solved this problem in the package "poppr"<br class="">
(<a href="http://cran.r-project.org/package=poppr" class="">http://cran.r-project.org/package=poppr</a>). The function "aboot" will<br class="">
calculate bootstrapped nj and upgma trees for any genetic distance<br class="">
(<a href="http://rpackages.ianhowson.com/cran/poppr/man/aboot.html" class="">http://rpackages.ianhowson.com/cran/poppr/man/aboot.html</a>) (see the<br class="">
second example).<br class="">
<br class="">
It doesn't do njs at the moment, but I can easily make a patch for that.<br class="">
<br class="">
Cheers,<br class="">
Zhian<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On Apr 7, 2015, at 03:00 ,<br class="">
<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org" class="">adegenet-forum-request@lists.r-forge.r-project.org</a> wrote:<br class="">
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Today's Topics:<br class="">
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1. conversion genind to loci (Virgilio Massimiliano)<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Mon, 6 Apr 2015 13:48:32 +0000<br class="">
From: Virgilio Massimiliano <massimiliano.virgilio@africamuseum.be><br class="">
To: "adegenet-forum@lists.r-forge.r-project.org"<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><adegenet-forum@lists.r-forge.r-project.org><br class="">
Subject: [adegenet-forum] conversion genind to loci<br class="">
Message-ID: <702BA0C8-1B27-4C0E-8E1C-41E36FADFB65@africamuseum.be><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
hi,<br class="">
I?m trying to make a bootstrapped njt on msat data,<br class="">
as far as I can understand, it?s not possible to bootstrap my loci<br class="">
starting from a genind object and this:<br class="">
<br class="">
myBoots <- boot.phylo(NJtree, data_genind@tab, B =100, function(xx)<br class="">
njs(dist(xx)))<br class="">
<br class="">
shouldn?t be correct as it bootstraps alleles (data_genind@tab)<br class="">
<br class="">
<br class="">
So I?m trying to convert my genind data into loci using genind2loci and<br class="">
read.loci :<br class="">
<br class="">
<br class="">
library(adegenet)<br class="">
data <- read.genetix("data.gtx")<br class="">
data_loci<-genind2loci(data)<br class="">
write.csv(data_loci, file = "data_loci.csv")<br class="">
library(pegas)<br class="">
data_pegas<-read.loci(file = "data_loci.csv", loci.sep = ",")<br class="">
<br class="">
and then get the tree (based on Fst, but it doesn?t work either with<br class="">
distances)<br class="">
<br class="">
pairFst <- pairwise.fst(data, res.type="matrix", truenames=TRUE)<br class="">
<br class="">
library(ape)<br class="">
njtreFst_pop <- njs(pairFst)<br class="">
myBoots <- boot.phylo(njtreFst_pop, as.matrix(data_pegas), B = 3,<br class="">
function(xx)<br class="">
njs(dist(xx)))<br class="">
<br class="">
but it doesn?t seem to work (I?m attaching the input file) and I get<br class="">
only error messages no matter what I try...<br class="">
<br class="">
What am I doing wrong? Is there a simpler way of getting bootstrapped<br class="">
msat loci starting form a genind object?<br class="">
<br class="">
greeting and many thanks in advance<br class="">
<br class="">
Massi<br class="">
<br class="">
<br class="">
<br class="">
__________________________________<br class="">
Massimiliano Virgilio, PhD<br class="">
<br class="">
Royal Museum for Central Africa<br class="">
<br class="">
Joint Experimental Molecular Unit (JEMU)<br class="">
<br class="">
Leuvensesteenweg 13, B-3080 Tervuren, Belgium, +32 (0) 27695366<br class="">
<br class="">
<br class="">
massimiliano.virgilio@africamuseum.be<mailto:massimiliano.virgilio@africa<br class="">
museum.be><br class="">
<br class="">
http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/<br class="">
<br class="">
http://jemu.myspecies.info<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
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