Hi, I have a dataset of roughly 7000 trees in newick format that I have loaded into R. Each tree has 5 tips, each representing a species. As the trees are not rooted, I am trying to root the trees using one of the species (AGAP) as the outgroup. However, when I run the root function like so:
x <- root(nh.tree.list[], outgroup = "AGAP")
The tree does indeed shift so that the node below the tip AGAP is at the base of the tree, but the tree remains unrooted (which I can confirm using the is.rooted command). This tree in question in newick format is:
I need to root the trees as the analysis I intend to do requires rooted trees. In case it helps, these trees were created from multiple sequence alignment fasta files, using neighbour joining methods (njs function). I cannot fathom why the trees aren't being rooted. Can anyone shed any light on this? Thanks.