Status

In view of the closure of CIPRES on 3/31/2026, we have created a new tool for downloading CIPRES folders. You do not need a Globus account, but you must install a Globus Connect Personal application to use the tools. Instructions are available.

Phoenix Bioinformatics will end its partnership with CIPRES as of September 30, 2025. As a result, CIPRES users will no longer be able to access compute time by purchasing a subscription. 

Existing Users: Any existing compute time will be extended automatically to 3/31/2026, when CIPRES operations are expected to cease. If you need more compute time, please do not create a new account. Instead, contact us at cipresadmin@sdsc.edu and let us know your needs. We will provide additional time at no cost if possible.

New users: accounts can still be created, and will receive 1000 hours of free compute time through 3/31/2026 when CIPRES operations are expected to cease. If you have questions, please contact us.

All jobs that could enter the maintenance period will be held in the queue until the maintenance is complete.

Emergency maintenance is complete..

We regret to announce that CIPRES will end operations on March 31, 2026.
New subscriptions will continue to be accepted until September 30, 2025, but the period of service will be gradually reduced from one year to six months. User files will be retained for 30 days after the end of production to allow you to retrieve any that you want to retain.

The CIPRES team – Mark Miller, Mark Zhuang, and myself – have appreciated the opportunity to help thousands of users around the world advance the sciences of evolution and population biology. and wish you continued success in your endeavors.

Please feel free to contact us at cipresadmin@sdsc.edu if you have any questions.

Wayne Pfeiffer
CIPRES Project Leader

Maintenance on Popeye is complete, and MrBayes jobs are running there again.

The system was down due to an unexpected issue. All systems are functioning normally now.

CIPRES now offers two new ASTRAL codes from the new ASTER package developed by Chao Zhang and Siavash Mirarab.
The code developers recommend that all ASTRAL users switch to the new codes: ASTRAL-Hybrid or ASTRAL-PRO.

ASTRAL-Hybrid is an upgraded, faster version of ASTRAL. It takes into account gene tree branch lengths and branch supports, making ASTRAL-Hybrid more accurate than ASTRAL.

ASTRAL-PRO is a special-purpose version of ASTRAL for PaRalogs & Orthologs. This is suitable for species tree inference from multi-copy gene family trees

CIPRES announces the release of Pythia, a code to evaluate how hard it will be to infer a tree from your matrix.

CIPRES now offers SPAdes for de novo genome assembly. SPAdes is designed for bacterial genomes, and has an option for metagenomics as well.
Information and example files can be found here.
Our recent survey showed user interest in genome assembly tools. Please let us know how we can best meet your needs.