<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
<div class="" style="word-wrap:break-word">hi,
<div class="">I’m trying to make a bootstrapped njt on msat data,</div>
<div class="">as far as I can understand, it’s not possible to bootstrap my loci starting from a genind object and this:</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">myBoots <- boot.phylo(NJtree, data_genind@tab, B =100, function(xx) njs(dist(xx)))</div>
<div class=""><br class="">
</div>
<div class="">shouldn’t be correct as it bootstraps alleles (data_genind@tab)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">So I’m trying to convert my genind data into loci using genind2loci and read.loci :</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
<div class="">
<div class="">library(adegenet)</div>
<div class="">data <- read.genetix("data.gtx")</div>
<div class="">
<div class="">data_loci<-genind2loci(data)</div>
<div class="">write.csv(data_loci, file = "data_loci.csv")</div>
<div class="">library(pegas)</div>
<div class="">data_pegas<-read.loci(file = "data_loci.csv", loci.sep = ",")</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">and then get the tree (based on Fst, but it doesn’t work either with distances)</div>
<div class=""><br class="">
</div>
<div class="">pairFst <- pairwise.fst(data, res.type="matrix", truenames=TRUE)</div>
<div class=""><br class="">
</div>
</div>
</div>
<div class="">
<div class="">library(ape)</div>
<div class="">njtreFst_pop <- njs(pairFst)</div>
<div class="">
<div class="">myBoots <- boot.phylo(njtreFst_pop, as.matrix(data_pegas), B = 3, function(xx)</div>
<div class=""> njs(dist(xx)))</div>
<div class=""><br class="">
</div>
</div>
</div>
<div class="">but it doesn’t seem to work (I’m attaching the input file) and I get only error messages no matter what I try...</div>
</div>
<div class=""><br class="">
</div>
<div class="">What am I doing wrong? Is there a simpler way of getting bootstrapped msat loci starting form a genind object?</div>
<div class=""><br class="">
</div>
<div class="">greeting and many thanks in advance</div>
<div class=""><br class="">
</div>
<div class="">Massi</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""></div>
</div>
<div class="" style="word-wrap:break-word">
<div class=""><br class="">
<div class="">
<div class="" style="color:rgb(0,0,0); letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; word-wrap:break-word">
<span class="x_Apple-style-span" style="border-collapse:separate; border-spacing:0px">
<div class="" style="word-wrap:break-word"><span class="x_Apple-style-span" style="border-collapse:separate; orphans:2; text-indent:0px; widows:2; border-spacing:0px">
<div class="" style="word-wrap:break-word"><span class="x_Apple-style-span" style="border-collapse:separate; orphans:2; text-indent:0px; widows:2; border-spacing:0px">
<div class="" style="word-wrap:break-word"><span class="x_Apple-style-span" style="border-collapse:separate; orphans:2; text-indent:0px; widows:2; border-spacing:0px"><span class="x_Apple-style-span" style="border-collapse:separate; orphans:2; text-indent:0px; widows:2; border-spacing:0px"><span class="x_Apple-style-span" style="border-collapse:separate; orphans:2; text-indent:0px; widows:2; border-spacing:0px"><span class="x_Apple-style-span" style="border-collapse:separate; orphans:2; text-indent:0px; widows:2; border-spacing:0px"><span class="x_Apple-style-span" style="border-collapse:separate; orphans:2; text-indent:0px; widows:2; border-spacing:0px">
<div class="" style="word-wrap:break-word"><span class="x_Apple-style-span" style="border-collapse:separate; orphans:2; text-indent:0px; widows:2; border-spacing:0px">
<div class="" style="word-wrap:break-word"><span class="x_Apple-style-span" style="border-collapse:separate; orphans:2; text-indent:0px; widows:2; border-spacing:0px">
<div class="" style="color:rgb(0,0,0); font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-transform:none; white-space:normal; word-spacing:0px; word-wrap:break-word">
__________________________________</div>
<div class="" style="color:rgb(0,0,0); font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-transform:none; white-space:normal; word-spacing:0px; word-wrap:break-word">
<font class="x_Apple-style-span" color="#004D95"> Massimiliano Virgilio, PhD <br class="">
<br class="">
Royal Museum for Central Africa <br class="">
<br class="">
</font></div>
<div class="" style="word-wrap:break-word"><font class="x_Apple-style-span" color="#004D95">Joint Experimental Molecular Unit (JEMU)</font></div>
<div class="" style="color:rgb(0,0,0); font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-transform:none; white-space:normal; word-spacing:0px; word-wrap:break-word">
<font class="x_Apple-style-span" color="#004D95"><br class="">
</font></div>
<div class="" style="color:rgb(0,0,0); font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-transform:none; white-space:normal; word-spacing:0px; word-wrap:break-word">
<font class="x_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>
<div class="" style="color:rgb(0,0,0); font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-transform:none; white-space:normal; word-spacing:0px; word-wrap:break-word">
<font class="x_Apple-style-span" color="#004D95"><br class="">
</font></div>
<div class="" style="word-wrap:break-word"><font class="x_Apple-style-span" color="#004D95"><a href="http://jemu.myspecies.info" class="">http://jemu.myspecies.info</a></font></div>
<div class="" style="color:rgb(0,0,0); font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-transform:none; white-space:normal; word-spacing:0px; word-wrap:break-word">
<font class="x_Apple-style-span" color="#2900D2"><br class="">
</font></div>
</span></div>
</span></div>
</span></span></span></span></span></div>
</span><br class="x_Apple-interchange-newline">
</div>
</span><br class="x_Apple-interchange-newline">
</div>
</span><br class="x_Apple-interchange-newline">
</div>
<br class="x_Apple-interchange-newline">
<br class="x_Apple-interchange-newline">
</div>
<br class="">
</div>
</div>
</body>
</html>