Status

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. 

MrBayes runs at CIPRES will now be as much as 1.5 times faster by using Simons Foundation's Popeye cluster.

We are grateful to Simons Foundation for allowing us to access this useful resource.

CIPRES now offers StatAlign a Bayesian program that allows multiple alignments, phylogenetic trees and evolutionary parameters to be co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable quantification of the uncertainty in these estimates.

PREQUAL is a tool to do PREalignment QUALity screening of sequnces for sequnece alignment.

Divvier is a tool for filtering or partially filtering out non-homologous sections from aligned sequences.

Muscle 5.1 (which has parallel options) is now available.