plot and show support values in consensus tree from n nj euclidean distance matrix replicates

Question

[jlsovaz]

Hello,

I have a problem trying to show support values in my consensus tree.

I have 100 different trees (dendrograms) created using nj with euclidean matrix distances.

I would want to create a consensus tree combining all these trees and add the proportion values (number of trees to the total) that support each branch of the topology of the resulting tree. I can create the majority-rule consensus tree using the function consensus (with p = 0.5) from ape package, but I can't find how to show the support values.

Thank you in advance,

Jose

Answer 1

[Joseph Hughes]

Using the boot.phylo function in the ape package in R, you can do the following:

data(woodmouse)
fun <- function(x) as.phylo(hclust(dist.dna(x), "average"))
tree <- fun(woodmouse)
bstrees <- boot.phylo(tree, woodmouse, fun, trees = TRUE)$trees
boot <- prop.clades(tree, bstrees)
plot(tree)
drawSupportOnEdges(boot)

Answer 2

[jlsovaz]

Thank you Joseph, it was useful and finally I could add the support values to my tree.

Kind regards,

Jose