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...") library(ctc) write.table(as.phylo(hc2Newick(fit), file="C:/path/output.txt",row.names=FALSE,col.names=FALSE)) Would anyone have an idea about how to make this work? Thanks so much in advance! Julian -- View this message in context: http://r.789695.n4.nabble.com/Hclust-tree-to-Figtree-w-branch-lengths-tp4655990.html Sent from the R help mailing list archive at Nabble.com.

...ral state probabilities state.probs pie.probs<-t(state.probs) pr<-apply(t(state.probs), 1, which.max)#max probability tree$node.label<-pr #labels the nodes with the character states write.tree(tree, file="T")#exports tree with nodes character states to directory #configuration in figtree - node label display label #tree pie charts pdf("TREE_PLOT.pdf", height=11, width=8.5) plot(tree ,cex=.8) nodelabels(pie=pie.probs,piecol=c("blue","red","yellow"), cex=.5) dev.off() [[alternative HTML version deleted]]