On 14 Dec 2016, at 15:33, Joseph W. Brown <josep...@umich.edu> wrote:

> I wonder if reading in a Nexus file with a translation table bypasses this 
> problem?


If I try read.nexus with a TAXLABELS entry, it still (oddly) results in a 
multiPhylo structure of the same size as before running .compressTipLabel. 
However, when I then do .compressTipLabel() it only takes a moment. My guess is 
this is something to do with skipping the renumbering process. It would be nice 
to have the option in both read.nexus and read.tree, so that I don’t have to 
allocate memory (many GB in my case) for the intermediate step.


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