Collapse a phylogenetic clade by support values

node_collapse

#Code to collapse a phylogeny by a tree's support values, when nodes have support value names
#tree = phylogenetic tree, cutoff = support value cutoff (can be changed or made into a vector)

require(ape)
h <- which(tree$node.label < cutoff)
nodes <- matrix(h + Ntip(tree))
nodes <- nodes[-1]
k <- matrix(tree$edge[,2])

j <- matrix(nrow = length(i), ncol = 1)

for (i in 1:length(nodes)){
  j[i] = which(k == nodes[i]) 
}
tree$edge.length[j] <- 0

newtree <- di2multi(tree)