[Phylobase-devl] Urgent! problems with installing

Steve Kembel skembel at berkeley.edu
Thu Jul 3 00:21:39 CEST 2008

Hi Marguerite,

There seems to be an even newer version of read.nexus on the ape svn  
server (version 2.2-1), the changelog says that version fixed a bug in  
read.nexus, and read.tree also seems to have been updated for 2.1-2.  
Does 2.2-1 work for you?

There are some notes in the changelog for ape about updates to  
read.nexus... the following might be relevant. Emmanuel probably has  
further insights:
Version 2.1-2:
read.nexus() now returns a modified object of class "multiPhylo" when  
there is a TRANSLATE block in the NEXUS file: the individual trees  
have no 'tip.label' vector, but the list has a 'TipLabel' attribute.  
The new methods '$' and '[[' set these elements correctly when  
extracting trees.

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