Here is a tree reader to make you smile when you are stuck with errors for apparent singleton nodes: Liam Revell's robust Newick (~phylogenetic) tree reader 'read.newick':
description: http://blog.phytools.org/2013/06/robust-newick-tree-reader.html
the code: http://www.phytools.org/read.newick/v0.5/read.newick.R
This was able to read a large (originally phylomatic) tree of ~5,000 species that the 'ape' package couldn't and that was too big for manual editing.
