Reuse Barriers

This page is a developing list of practical barriers to reuse of evolutionary data, in particular phylogenetic data and trees. Since digital access to trees (and data) is normally the starting point for reuse, barriers to the digital availability, findability, and free access to trees, such as barriers to deposition in a digital archive, are deliberately included in the scope here.

Incorrect support of exchange standards

The most widely used exchange standard for phylogenetic data is NEXUS. NEXUS files are difficult to validate for compliance with the standard, and some programs either don't support the standard, or their support is incorrect. Digital archives cannot support all possible exchange formats and the variations of their implementations. For example, TreeBASE has had to resort to supporting only NEXUS files produced by the Mesquite tool. This makes digitally archiving and sharing of trees for reuse burdensome and error-prone for users of all other programs.

Examples:

• WinClada sometimes produces faulty NEXUS files. For example, WinClada's method of indexing character labels and states is wrong.
  • Symptom: "I keep encountering an error when I try to upload the file to TreeBASE. The file has been created by WinClada."
  • Recommended workaround: Get Mesquite to open the file -- check that everything looks right -- and then have Mesquite save the file. Submit to TreeBASE.