CIPRES Portal v 1.13 (version history)

NEW FEATURES: BOOTSTRAP-RAxML REST Service; Support for Large File Uploads

The CIPRES Portal is currently under development. The portal is built on top of the CIPRES software libraries. The CIPRES project focuses on the inference of large trees. All software developed directly by the project is free and platform independent, and we are working on pain-free installation procedures. A MAC version with an installer is now available. The portal lets you explore software that has been adapted to the CIPRES system without having to install it on your own machine. Calculations are carried out on the CIPRES cluster, at the San Diego Supercomputer Center.

Tools for Sequence Alignment: ClustalW (fasta format accepted).

Tools for Large Tree Inference (REC I DCM3 boosting is available for RAxML and PAUP).

Note that each of the tree inference methods can be used as a standalone or in combination with a meta-heursitic to extend the range of problems that can be analyzed. The CIPRES portal is currently using Rec-I-DCM3 for RAxML and PAUP. Rec-I-DCM3 is a divide-and-conquer technique as a higher level algorithm. For details refer to the discussion of Disk Covering Methods (pdf) and a specific discussion of Rec-I-DCM3 (pdf). An implementation of the Nixon's ratchet [Nixon, K. C. (1999) Cladistics 15: 407-414.] is available for PAUP.

Requirements:
Input: A matrix of DNA (All) or AA (PAUP,RAxML) sequence or characters (PAUP) in NEXUS; PHYLIP; or HENNIG86 format. A starting tree is not required, but you can improve upon an initial estimate of a tree. To do this, simply include this estimate in a Trees block in the NEXUS file. If there are multiple trees in the Trees block, the first one will be used.

Limitations:
Configuration of some parameters by users is now supported, although some options are not yet supported. Many PAUP options that can be accessed from within the Nexus file in a local installation are not supported at this time. Because the cluster is a shared resource, jobs that run over 72 hours are subject to being killed before they return results. How long will my job take to run? If you think your job may run too long, please contact Lucie Chan for assistance.

Output:
Output can be monitored in real time using the progress viewer link provided after submission. Results are returned to the user as a file in valid NEXUS format. A link to this file is displayed in the browser (HTML), and mailed to the user. Results will be stored for 7 DAYS ONLY, then will be purged.

Current Usage Statistics: here.

Features that are coming:
The following features are planned for release in the near future:

• Improved Job Queing Strategies
• New Tools for Sequence Alignment
• New Tool for Creating Model Data

Please send us your feature requests

CIPRES is a Collaboration of the Following Institutions:
American Museum of Natural History, Florida State University, New Jersey Institute of Technology, North Carolina State University, Rice University, San Diego Supercomputer Center, Texas A&M, University of Arizona, University of British Columbia, University of California at Berkeley, University of California at San Diego, University of Connecticut, University of Pennsylvania, Univ. of South Carolina, University of Texas at Austin, and Yale University. xhtml | css