Cipres Web Portal

In the CIPRES portal v. 2.0, commands that would instruct programs from within Nexus are supported; this was a key request of our users of CIPRES Portal v 1.13. We believe that in most cases, the use of command blocks in Nexus files is the preferred way to conduct analyses. However, given how diffiult Nexus files are to parse, we expect this will raise a number of other issues. 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. 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.