phylotate provides functions that allow you to read and write NEXUS and Newick trees containing annotations, including those produced by MrBayes.
It does this by extending ape's phylo object type with
extra data members containing per-node annotation information. This
information is stored in such a way that it can be manipulated easily
and will survive most manipulations using standard ape functions
(e.g. reorder, chronopl).
See the documentation for the parse_annotated function
for more information on how annotations are stored internally.
The functions you probably want to use for most things are
read_annotated and write_annotated.