Potential bug when reading Mesquite formatting from nexus files

[Carolyn]

Hello,

I recently got the following error when trying to plot a phylogenetic tree from a nexus file called Eucalypt_Bayes_dated_character_mapped.nex, which I downloaded from CSIRO.

plot(euc.tr)
Error in plot.phylo(euc.tr) : tree badly conformed; cannot plot. Check the edge matrix.

A commenter on Stack Overflow helped me plot the tree by replacing and removing some text in the nexus file, but suggested that there might be a bug in read.tree when trying to parse Mesquite formatting from a nexus file, which might cause the edge matrix to have strange numbers.

Thanks,
Carolyn

[Emmanuel Paradis]

Hi,
It's a feature of read.nexus which is mentioned in the help page:

If a TRANSLATION table is present it is assumed that only the tip
labels are translated and they are all translated with integers
without gap.

This makes decoding of the trees much faster and it is compatible with most NEXUS trees.
Emmanuel