Dear Gwennaël,
the bootstrapping function is fine, it is just a problem with the
plotting. Can you try this function, it should work:
plotBSNew - function (tree, BStrees, type = unrooted, bs.col = black,
bs.adj = NULL, ...)
{
prop.clades - function (phy, ..., part = NULL, rooted = FALSE)
{
Dear All
I am constructing maximum parsimony trees:
library(phangorn)
primates = read.phyDat(primates.dna, format=phylip, type=DNA)
dm = dist.dna(as.DNAbin(primates))
treeNJ = NJ(dm)
treePars = optim.parsimony(treeNJ, primates)
##and
treeRatchet = pratchet(primates, trace = 0)
, and I would
