phangorn - a really good tools for Phylogenetic analysis in R

1. http://bioinformatics.oxfordjournals.org/content/27/4/592.full

2. http://cran.r-project.org/web/packages/phangorn/

data(yeast)

tree <- NJ(dist.logDet(yeast))

fit <- pml(tree, yeast, k=4, inv= .2)

fit <- optim.pml(fit, optNni=TRUE, optGamma=TRUE, optInv=TRUE, model=“GTR”)

BS <- bootstrap.pml(fit, optNni=TRUE)

plotBS(fit$tree, BS, type = “phylogram”)