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mbrazeau / morphy.archive

Morphy releases are archived here. This project serves as the root folder for all of the source projects in Morphy.
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Writing tree to nexus file #3

Closed ms609 closed 4 years ago

ms609 commented 4 years ago

When I use save=trees.tre, the TRANSLATE table include spaces between genus and species in taxon names, surrounding space-bearing taxa in 'single quotes'.

I can only open this file using ape::read.nexus if I replace these spaces with underscores.

I'm not sure whether this is an issue with Morphy or with R's ape package... should Morphy be writing underscores, or does the NEXUS specification allow for spaces (in which case I'll post an issue with 'ape'!)

mbrazeau commented 4 years ago

That appears to be a limitation of ape. Morphy does extremely little in terms of writing/reading file data itself. Nearly all of that is handled by the Nexus Class Library which is about as standard-conforming as anything gets.