Dear Dr. Jombart and adegenet users,


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


	[[alternative HTML version deleted]]

