Zephyr: a Mesquite package for interacting with external phylogeny inference programs

Current release version: 2.01


Lead developers

David R. Maddison, Oregon State University
Wayne P. Maddison, University of British Columbia

Other contributors
Kipling W. Will, University of California at Berkeley (design and troubleshooting for TNT interactions for version 1.1 of Zephyr)


Zephyr is a Mesquite package that provides tools for interacting with phylogeny inference programs such as RAxML and GARLI. From within Mesquite one can ask Mesquite to send a matrix to the external program, have Mesquite monitor the run as it is going (including, on occasion, seeing the latest tree), and then harvest the results back into Mesquite automatically once the analysis run is done. In addition, Zephyr allows you to conduct a Swofford-Olsen-Waddell-Hillis (SOWH) test from within Mesquite.

Currently, Zephyr supports the following inference programs:
  • GARLI (either on your local machine or CIPRes)
  • RAxML (either on your local machine or CIPRes)
  • PAUP* (parsimony, likelihood, distance, or SVD Quartets analyses)
  • TNT

Zephyr 2.01 requires Mesquite 3.31 or later.

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More information is available by clicking on the links at the left.