I have been using R to create and manipulate phylogenetic trees for a while, but I was wondering what the differences are between the rooting functions in different packages,
I have attached an example. Every tree looks slightly different, and the tree created by
ggtree::reroot seems best to me. Could anyone explain the differences?
tree <- read.tree(text = "(t6:0.3806255851,(t7:0.5440872659,(t5:0.6203179485,t1:0.7089423968):0.3421749519):0.2618428892,((t4:0.5886056426,t3:0.8614832051):0.09094934678,(t8:0.6766210056,t2:0.1412485428):0.4451906278):0.2356684168);") par(mfcol=c(2,2), mar=c(0.5,0.5,1.3,0.5)) plot(tree) nodelabels() title("original") tree1 <- ape::root(tree, node = 11) plot(tree1) nodelabels() title("ape::root") tree2 <- ggtree::reroot(tree, 11) plot(tree2) nodelabels() title("ggtree::reroot") tree3 <- phytools::reroot(tree, 11) plot(tree3) nodelabels() title("phytools::reroot")
Any explanation would be greatly appreciated.