On 14 Dec 2016, at 21:06, Emmanuel Paradis <emmanuel.para...@ird.fr> wrote:

> If the trees are in a NEXUS file with a TRANSLATE block, then the output is a 
> compressed list. So applying .compressTipLabel returns the list unmodified 
> (which should be almost instantaneous).

Ah, I see what I was doing wrong. I used a BEGIN TAXA;TAXLABELS ... END; block, 
rather than a TRANSLATE block within the TREES block. The read.nexus() function 
now works as Joseph Brown surmised. So the easiest way for me to do this is 
simply to use a nexus format trees file.

Thanks

Yan
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