CIPRES Portal V 1.15 (version history)

 

The CIPRES Portal V. 1.0 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.

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.

CIPRES Portal V 2.0 (version history)

The CIPRES Portal V. 2.0 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 2.0 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 called webtooldev.

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.

Tools for Sequence Alignment: ClustalW (Both); Contralign (Portal2); MUSCLE (Portal2); MAFFT (Portal2), PROBCONS (Portal2), PROBALIGN (Portal2). FSA is coming soon.

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:

• Better data parsing/identification
• Ability to download all results files with a single click
• BEAST

Please send us your feature requests