On 4 Jan 2017, at 16:03, Emmanuel Paradis <emmanuel.para...@ird.fr> wrote:

> This is a known feature of read.nexus(), see ape's FAQ:
> http://ape-package.ird.fr/ape_faq.html#Bayestrees
> This explains how to fix the problem.

Oh, sorry. I should have read the FAQ before posting. If you are thinking about 
adding a force.multi option to read.nexus, is it worth also adding a 
tip.labels.start.at.zero option to read.nexus too, and just adding that little 
code snippet right at the end of the the read.nexus code?

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