I am using phangorn, maximum likelihood to estimate tree.
optim.pml process, I used rearrangement = "stochastic",
fit <-optim.pml(fit, multicore=TRUE, rearrangement = "stochastic")
so when bootstrap I should use optnni = TRUE or go straight forward? What is the difference, and the
bs <- bootstrap.pml(fit, bs=100, optnni = TRUE)
Sorry for the silly question but I cannot find an answer by search.