[R-sig-genetics] Computation of bootstrap support values for UPGMA

[Jombart, Thibaut]

Hello, 

this is clearly an adegenet-related question. Please repost on the adegenet forum.

Cheers
Thibaut
________________________________________
From: r-sig-genetics-bounces at r-project.org [r-sig-genetics-bounces at r-project.org] on behalf of Benjamin Alric [benjamin.alric at imbe.fr]
Sent: 18 June 2013 09:00
To: r-sig-genetics at r-project.org
Subject: [R-sig-genetics] Computation of bootstrap support values for UPGMA

Dear Dr. Jombart and adegenet/adephylo users,

Sorry for the duplication between adegenet and adephylo list but not
knowing which could help my problem, I send this message in both.

I have microsatellite data set (8 locis in column and 24 population in
row) on the hybridizing populations of Daphnia in the three lakes.

I assigned parental species and hyrids cluster by DAPC.

Then, I made UPGMA from Nei's genetic distance according to the script
below.

#library (ade4)

#library (adegenet)

genetDaph<-import2genind("UPGMA_Genetix_adegenet.gtx",package="adegenet")

genetDaph2<-genind2genpop(genetDaph)

dist1<-dist.genpop(genetDaph2,method=1)

clust<-hclust(dist1,method="average")

plot(clust)

Currently, I would like determined the bootstrap support values of this
tree.

However, I do not found such a function in 'adegenet' package.

Can we made a bootstrap on tree from 'adegenet' package ?

Besides, I seek in 'adephylo' package without success.

Then, I found 'ape' package.

In this one, we can work from dist.gene, but I do not find how convert
'genetDaph2' in dist.gene.

Somebody have an idea or have already computed bootstrap support values
of tree with R?

Thank you in advance for your help.

Best regards,

Benjamin ALRIC

--
Benjamin Alric,PhD
UMR 7263-CNRS / 237-IRD - Institut Méditerranéen de Biodiversité et d'Ecologie (IMBE)
Equipe "Ecologie des Eaux Continentales"
Aix-Marseille Université, Faculté des Sciences, site de St Jérôme
52 Avenue Escadrille Normandie Niémen
13397 Marseille cedex 20 - France


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