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).
Best,
Emmanuel
Le 14/12/2016 à 16:51, Yan Wong a écrit :
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?
Cheers,
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.
Thanks
Yan
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