CIPRES Science Gateway supports command blocks within Nexus when those blocks are supported natively by a program. This feature was a key request of CIPRES Portal1 users. We believe that in most cases, command blocks in Nexus files are the preferred way to conduct analyses. Nexus files aredifficult to parse, because there are so many formats used, and so many different ways to encode the information. The tool Format Validator is provided to help with this. Mark Holder created this tool for the CIPRES group, based on the NCL program of Paul Lewis (soon to appear as Phycas). While philosophically we favor more strict standards, each program here has its own philosophy and capabilities for Nexus interpretation. Accordingly, the documentation for each indvidual application should be the resource of first resort for issues that arise.
The original document specifying Nexus file formats is here [pdf].
If your NEXUS file is rejected please also try the Format Validator tool for help. Another resource is a list of formatting issues that we have run into from submissions to CIPRES Portal v 1.0. They can be found here, along with solutions.
If there is a tool or a feature you need, please let us know.
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