R help - Jan 2013 - Hclust tree to Figtree w/ branch lengths

Hi,

I'm doing hierarchical clustering, and want to export my dendrogram to a
tree-viewing/editing software. I can do this by converting the data to
Newick format (hc2Newick in ctc package), but I can't get branch lengths to
show in the resulting phylogram. I figured it might help to convert my
hclust object into a phylo object (as.phylo in ape package), but the
following lines give me this "Error in UseMethod("as.phylo") : no
applicable
method for 'as.phylo' applied to an object of class
"character":

data = read.table("C:/path/data.txt")
d <- dist(data, method = "euclidean")
library(ape)
fit <- as.phylo(hclust(d, method="ward")
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



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Hi,

This worked:

fit <- hclust(d, method="ward")
library(ape)
p <- (as.phylo(fit))
write.tree(p, file="MyNewick.tre")

Cheers,
J



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