Nexus format: If you are having trouble submitting a valid Nexus file, this page has some tips.

NEXUS files are notoriously difficult to parse, because there are so many formats that are used, and so many different ways to encode the information. Also, some programs are troubled by NEXUS that is not formally legal, while others are not. Mark Holder has led the CIPRES group's Nexus Parser program, based on the NCL program of Paul Lewis (soon to appear as Phycas). The CIPRES Portal2 offers NCL parser and the format validator tools to help users detect and resolve file format issues. Philosophically, we have adhered to more strict standards, for the most part, because we believe many relaxations of Nexus Standards can lead to inadvertent errors in the results set. In other words, you gave a command that was slightly different than the one you thought you gave.

If your NEXUS file is rejected please take a look at the suggestions below. You can grab the documents in [doc] or [pdf] if that suits you better. We provide several different archetypal errors, each of them we have seen in one or more files submitted to the site. The examples show the full range of error messages one might encounter. If they are not sufficient, please let us know. The document for Nexus file formats is here [pdf].

Some Key Things to Know:

In the CIPRES portal, commands that would instruct PAUP from within Nexus are removed by the Parser. Soon there will be an interface that allows you to instruct PAUP at a finer grained level, but for now it is not possible.

The parser currently has trouble with new symbols, even if they are not used in the Nexus file. It is best to just remove the symbols, if possible.

Nexus Errors We Have Seen:

Total files errors: 62
Possible parser errors: 9
Server issues*: 1

*Not reproducible

Error type 1. File type errors:

Error type 2. Parser problems:

Parser problems are errors in legal nexus that we can’t handle yet.

All examples so far are below.

Error type 3. Misspellings, misplaced semi colons, etc

Error Type 4.  Taxon naming errors: 8 examples

Error Type 5. Errors in GAP settings: 2 examples

Error Type 6.  Errors in state labels: 2 examples

Error Type 7. Symbol Issues: 20 examples

Error Type 8. Just plain illegal NEXUS

Error Type 9. Problems executing: 2 examples