Hi Yan,
Joseph was right. In read.nexus you need a TRANSLATE block, just a
TAXLABELS is not enough. Then read.nexus returns the compressed object and
is 10x faster to read in (for 1000 trees with 1000 taxa on my machine).
There is also the package rncl (Nexus Class Library), it is faster to read
in, even the pure R implementation with the TRANSLATE block is almost as
fast.
However the objects are actually quite a bit larger. It also stores the
edge matrix as doubles, and which I find dangerous.
Cheers,
Klaus

On Wed, Dec 14, 2016 at 4:44 PM, Yan Wong <y...@yanwong.me> wrote:

>
> 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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-- 
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/

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