Powering Phylogenetics and Population Biology Research

CIPRES provides access to a large number of compute-intensive phylogenetics and population biology codes run on high performance computers provided by the National Science Foundation. The CIPRES application ensures that users can analyze their data quickly and efficiently without having to install codes or learn how to submit jobs to a compute cluster through a remote scheduler. More than 30,000 researchers have used CIPRES since it was launched in 2010, and over 12,000 scholarly journal articles have been published using data generated by the system.


Up to 1,000 hours of compute time on CIPRES is absolutely free. Subscribing to CIPRES gives you additional computing time plus helps support ongoing CIPRES operations, such as maintaining and improving the existing interface, testing, benchmarking and releasing new tools, providing user support, monitoring and responding to interruptions in service, ensuring users have equal access to compute resources, and helping individual users with special job requirements. Subscriptions can be purchased from your grant with an institutional procurement card, or you can use a personal credit card (click here), or a purchase order (email [email protected] for details). Payment must be received before subscription access can be provided. If these options don’t meet your needs, please contact [email protected].


Support for this capability plus the low-cost of additional computing time (see pricing schedule) is made possible by a subsidy from the National Science Foundation’s ACCESS program (Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support).

The CIPRES model is based on a flat rate, renewable annual subscription. A free Level 1 subscription provides access to CIPRES codes, job submission tools, 150 GB free storage, user support, and 1000 core hours of compute time per year. Enhanced subscriptions provide the same benefits and access to more compute time. The subscription levels provide 10,000, 20,000, 50,000, 100,000, or 200,000 core hours of compute time per year.

It is possible to run your jobs through a cloud provider. However, this will require learning to use the command line interface, installing the tools you require, and benchmarking them so they run efficiently. The cost of running one CPU (provisioned like CIPRES) at AWS is 8.5 cents (US) per hour, and this does not include network and data storage charges. In this model, 5,000 core hours on a “bare metal” AWS instance will cost at least $425 plus the amount of time required to set up the instance and install the code. For $150, a subscription at CIPRES provides 11,000 hours of compute time, access to current tools, 150 GB data storage, a user-friendly point and click interface, and customer support.

You can also get your own ACCESS account and run jobs from the command line there if you are at a US institution. However, ACCESS accounts can only be requested by users in the US who have a Ph.D. or are at the Principal investigator level or higher in their organization. ACCESS accounts do not provide a user interface, but instead rely on command line usage. The user is responsible for installing all of the codes they require, and configuring them to run efficiently. CIPRES handles all this for you.

Usage is calculated based on the amount of compute time you consume in a calendar year. Your account is charged only for compute time you actually use. Most CIPRES jobs run on multiple processor cores, so your account will be charged for the number of compute cores your job used multiplied by the number of hours your jobs run. Further submissions from your account will be halted automatically when you reach your annual limit.

You can access more compute time by purchasing a new subscription at any time. Any user account can purchase a new subscription at any time. Should you require more than 100,000 hours for a year, please contact us.

Compute time available at the end of subscription year will not be carried over to the subsequent year, but the year begins on the date of the most recent purchase. So you can extend the availability by making an additional purchase. You will be granted a new allocation of 1,000 free hours once per year, and you may purchase a new subscription to access more hours.


“CIPRES has moved the needle in terms of the kinds of questions can be asked by field biologists”

“The computations took 6 minutes on CIPRES for my input file, while trying to run this on my PC it collapsed after 2 weeks! User friendly server …. which greatly facilitates research!”

“I’m in the jungles of Panama for fieldwork , can’t tell you how helpful it is to have this resource.”

“I am at a small regional university where I do not have access to the kind of computing power available at R1 universities. Therefore, my research program really benefits from this amazing resource.”

“The wall time for these data sets are 30 min (2000 Bootstrap reps) [on the CSG], but locally it would take 24 hours for each run. So, instead of 10 days to complete all the analyses with a few local computers, I have publication quality trees overnight.”

“It is hard for me to imagine how I could work at a reasonable pace, especially when things like manuscript or grant submission deadlines loom, without this resource. I am pushing now to submit a manuscript by Friday, and I am making multiple runs by RAxML and MrBayes each day, but all of which are necessary to get the final picture polished and submission-ready.”

“The functional capabilities in phylogenetics provided by the combination of high-performance computing resources and user-friendly interfaces at CIPRES allow a biologist to concentrate on hypothesis testing and “biological thinking”, rather than being forced to spend an inordinate amount of time fighting what are purely computer science associated issues to get at usable data in a reasonable amount of time.”