The phytools function read.newick is a slower, but slightly more robust Newick tree reader than read.tree in the ape package - specifically in that it permits certain types of 'badly conformed' Newick strings, such as those containing singleton nodes.
It's Achilles heel, however, has been that it does not permit a node label for the root node of the tree. The fix for this was simple and was supplied to me by Joseph Brown. The updated function code is here & also in the latest non-CRAN phytools version (phytools >= 0.4-23) here.
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