I have installed Bio::Phylo from CPAN. I will first try to get phyimport.pl up and running using the Bio::Phylo object model for nodes. If this works without too much trouble, I will use Bio::Phylo for PhyExport as well. This should allow more of the information related to the tree to be added to the database and exported to output files.
Bio::Phylo documentation.
Update:
I am getting the following error when trying to parse a NEXUS file
"Inappropirate ioctl for device"
I don't know what is going on with that. If I don't get this working quickly I will abandon Bio::Phylo.
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