On 14 Dec 2016, at 20:57, Emmanuel Paradis <emmanuel.para...@ird.fr> wrote:

> What is the size of your problem?

Erm, quite large. I am looking at tree comparison metrics for roughly 10,000 
trees with perhaps 10,000 tips on each, replicated several times. The newick 
files themselves take up gigabyes uncompressed. For this sized problem I’m 
likely to implement my own comparison metrics, but I want to trial this out 
with a tested library before rolling my own.

> Do you use a recent version of ape? This function was improved one or two 
> years ago.

Yes, 4.0.

But I’m happy for the moment to just leave this stuff running for days on a 
server, so it was just a quick suggestion really.

Thanks for the quick reply

Yan
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