CIPRES Portal V 1.15 has now ceased operations. (version history)

 

CIPRES Portal V 2.2 (version history)

The CIPRES Portal V. 2.2 is now in full release. It is built on a new architecture called the Workbench Framework. The new architecture allows us to provide users with a permanent data storage area, and allows us to expose all the command line options of any tool. The interfaces of the Version 2.2 Portal are based on PISE XML, and it is possible for anyone who takes a few hours to learn the specification to build a new interface or edit an existing one. Several community developers have contributed their tools to Version 2.0 portal using our build-and-test web server. Through a collaboration with Alexandrous Stamatakis and Wayne Pfeiffer, we now offer some very fast hybrid versions of RAxML and MrBayes.

Requirements:
Input: A matrix of characters in a format determined by the target software package. The NCLconverter, Format Validator, and Readseq tools are provided to assist users in interconvertng NEXUS,PHYLIP, and aligned fasta formats. Results are stored indefinitely.

Limitations:
In order to enabe all command line options, Portal2 does not support robust parsing. Instead the portal relies on the native formats required by individual packages. Because the cluster is a shared resource, jobs that run over 72 hours are subject to being killed before they return results. If you think your job may run too long, please contact Mark Miller for assistance.

Tools for Sequence Alignment: ClustalW, Contralign, FSA, MUSCLE, MAFFT, PROBCONS, PROBALIGN.

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

Note that PAUP and RaxML tree inference methods can be used as a standalone or in combination with a meta-heuristic to extend the range of problems that can be analyzed. The CIPRES portals currently provide 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.

Current Usage Statistics: here.

Features that are coming for Portal 2:
The following features are planned for release in the near future:

• Ability to download all results files with a single click
• BEAST

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