How to convert phylo object to hclust object in R
I think there several similar question but I can't solve my issue following with previous answer.
I am trying to convert phylo object to hclust object by following.
dna <- read.dna("my.dna.aln", format="fasta")
dist <- dist.dna(dna)
dna.nj <- nj(dist)
dna.hcl <- as.hclust(dna.nj)
error in as.hclust.phylo(dna.nj) : the tree is not ultrametric
I really need to convert hclust rather than dendrogram. When I tried to use chronopl it gives me following error
chronopl(dna.nj, 0, age.min = 1, age.max = NULL,node = "root", S = 1, tol = 1e-8,CV = FALSE, eval.max = 500, iter.max = 500)
error in chronopl(dna.nj, 0, age.min = 1, age.max = NULL, node = "root":
at least one terminal branch is of length zero:
you should remove it to have a meaningful estimation.
Do you have any suggestion. Thank you, Taiki
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engelbert_buxbaum •
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ttsutsui1028 •
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ttsutsui1028 •
2 answers
Did you check this? https://www.rdocumentation.org/packages/ape/versions/5.0/topics/as.phylo
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felipelira3 •
Approach the problem from the other end:
dist.dist <- as.dist(dist)
DNA.hc <- hclust(dist.dist, method = "average")
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engelbert_buxbaum •
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