# PAUP Paup 4 is available to all users on the cluster. Interactive paup jobs can be run from a qlogin session, and batch jobs may be submitted with the runpaup and runpauprat commands. Batch jobs will continue to run even if you log out. The paup, runpaup, and runpauprat commands are available in the PATH by default. ``` runpaup ``` PAUP (Phylogenetic Analysis Using Parsimony) uses NEX files as input. Example files can be found at /share/apps/paup/Sample\_NEXUS\_data/. To run PAUP on a nexus file called myfile.nex, type: ``` runpaup myfile.nex runpauprat ``` The cluster also provides the runpauprat command for submitting PAUPRat jobs. PAUPRat is a tool to implement Parsimony and Likelihood Ratchet searches using PAUP. To launch a batch PAUPRat job with an input file called myfile.nex, type: ``` runpauprat myfile.nex ``` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://usdrcg.gitbook.io/docs/practice/about-legacy/geant4.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.