The CIPRES Software Effort
A key deliverable of the CIPRES project is freely-available, platform-independent software that can be installed on a laptop or desktop computer or run on a large supercomputer. To achieve this deliverable, the CIPRES software team, led by Mark Holder is actively developing software tools to serve practicing systematists (particularly those with large data-sets), computational systematists who implement algorithms, and algorithm designers. The basis for the enabling technology is a flexible, efficient library that allows for cooperation/communication between diverse phylogenetic modules. The libraries will make it possible for developers within the community to easily link their software to the software of other developers.
Biologists can access the CIPRES software services through multiple front-ends. Modules that allow the widely-used Mesquite software package to access CIPRES services will be released in Fall of 2006. The visual programming environment Kepler allows users to construct workflow's by arranging and linking icons which represent distinct computational tasks. In addition to Mesquite and Kepler, the CIPRES software team has produced a simple Java application that uses CIPRES services to implement the recursive-iterative-DCM3 methods of Usman, Warnow, et al. All CIPRES software is still in the testing/pre-release stage.
Package 1: The CIPRES libraries
Package 2: CIPRES-KEPLER
- Macintosh users can download a (pre-release, testing) version CIPRES in Kepler workflow:
- (A licensed version of PAUP is required)
- Instructions for Installation are pdf and doc.
- If you download the software, fill out this questionnaire, and enter in a drawing to win an iPOD
NEED MORE INFORMATION?
- The CIPRES-Kepler functionality was presented at the 2006 Evolution meetings in Stony Brook, NY by Zhijie Guan. For more information, see:
- A flash movie demonstration of the CIPRES in Kepler.
- Zhijie Guan's PowerPoint presentation of CIPRES in Kepler (given at the 2006 Evolution meetings).
The software development effort is a collaboration between developers at SDSC (Terri Liebowitz, Lucie Chan, Zhijie Guan) and systematists (Mark Holder, Paul Lewis, David Swofford, Wayne Maddison, David Maddison, Peter Midford, and Rutger Vos).
CIPRES software links: