Hi,
Brian is 100% right about interpreting bootstrap values. When the tree is input
into R with read.tree() or read.nexus(), these values are attached to the nodes
but they relate to their subtending branches. The function root() has the
option 'edgelabel' to specify whether these node labels
You might need to reindex each time, something like (pseudocode):
bad.nodes <- function_to_get_node_numbers_with_support_less_than_90(phy)
while(length(bad.nodes>0)) {
phy <- collapse.to.star(phy, bad.nodes[1])
bad.nodes <- function_to_get_node_numbers_with_support_less_than_90(phy)
}
But
Dear all,
I'm surprised I could not find a simple function to do this in any of the
packages I know. I just want to take a tree with node labels (e.g.
bootstrap values from a RAxML analysis) and collapse all nodes with support
values below, say, 90%. I tried to do this recursively using
