Author Archives: Bob Thomson

About Bob Thomson

Assistant professor in the Department of Biology at University of Hawaii Manoa.

Has CIPRES helped you out?

cipresCipres is preparing their annual useage report which, among other things, helps determine the size of their XSEDE allocation from year to year. Please read the email from Mark Miller (copied below) and participate in their short survey (available at

Dear CIPRES Science Gateway User,

We need your help to keep the CIPRES Science Gateway operating. You received this email because you are one of the 2800+ users who submitted a job from the CIPRES Science Gateway during the past year. Each year we must report on user activities to continue receiving annual allocations of computer time for our Gateway.

In the last year, strong user response to this survey helped us increase the amount of time we received from the XSEDE allocations committee, and an NSF award to create a new set of CIPRES Web Services. Soon you will be able to access CIPRES through tools like Mesquite, or through scripts you write yourself, as well as through the browser interface.

Even if you just used it for a class, you can help by completing a brief survey (just a few questions) describing your activities on the CIPRES Science Gateway, and providing opinions about how the CIPRES Gateway should continue to operate.  The survey is located here:

The survey results help us continue to provide the community with easy access to computational resources for phylogenetic programs, and help us plan for sustainability of the resource. It requires only a few minutes to complete, but your feedback is a key element in justifying access to NSF resources.
If you do not wish to complete the survey, please help by sending me citations for any publications that were enabled by the CIPRES Gateway.
Thanks for your help,

Mark Miller
Principal Investigator

Student Presentations!

photos: Luke Mahler

New Website

Five years ago, I put together the first iteration of the Bodega Workshop’s website as a dirt-simple wiki hosted through the (Davis, CA-based) wikispot project. Our initial goals for the website were simple: provide an editable set of course materials for use during the workshop and accessible review materials for course participants afterward. A wiki-based system seemed ideal for this, instructors could easily add new content and (more importantly) the students could fix our errors. To get it launched that first year, Rich Glor, Brian O’Meara and I spent a big chunk of the workshop simply gathering up content and dumping it into the wiki framework. As the years have gone by, many people associated with the course have all pitched in to add content, revise outdated parts, and just clean things up. It’s been a great group effort.

About a year after first launching the website, we noticed that it was starting to get a fair bit more traffic than would be expected based on the number of people involved with the course. Since that time, the usership for the site has continued to grow and now averages a couple of hundred visitors a day—a small number in the scheme of things, but a much larger number than any of us initially expected. We have also been happy to see that the user community for the website is highly international (it varies through time, but the proportion of visits from outside of the US typically hovers around 50%).  Its good to see that course materials developed in the workshop get such wide use. 

Average daily visitors from 2008 to present. Spikes and dips associated with the March workshop and winter holidays are obvious, but what’s going on with those pre-holiday spikes in traffic?

Over the last five years, the content of the website has grown from that first single page to more than 200 and maintenance has become more unwieldy within the confines of the original wikispot framework. Furthermore, as fond as I am of the retro 90s “sea green and periwinkle” look that the website sports, I’ll grudgingly admit that we are far past due for a refresh. To remedy both of these issues, I’ve moved the site over to WordPress. Rich Glor kindly donated the use of our new domain, and I’m handling the hosting on my lab website’s server. A potential downside to this change is that we lose the wiki functionality where anyone can log on and make changes. That said, the group of active editors for the old wiki site has never been particularly huge, so this won’t have a large impact on site maintenance.

We of course still welcome any additional contributors to the site, whether you’re involved with the workshop or not. Please use the comments to note important typos or errors. I’ll be keeping an eye on things and will incorporate minor changes as necessary. Better still, get in touch with me and I’ll make an account for you. This way you can join the ranks of regular editors to the website. We would particular welcome input from anyone who has an interest in contributing new tutorials to the site or would like to contribute blog-style posts about emerging topics or other goings-on in phylogenetics. The course website gets used by a whole lot more people than attend the course, so it only makes sense that this wider community helps shape the content. In particular, I’d like to encourage former Bodega students to pitch in and contribute to the site, there’s around 400 of us out there at this point.

The old wiki site will stay up for a while, but won’t be updated anymore. Please update any bookmarks/RSS feeds to point to this site.

In other news, the 2013 workshop is now only a month away! We should see a flurry of updates from workshop planners, Brian Moore and Peter Wainwright; the workshop coordinator, Gideon Bradburd; and the rest of the instructors soon.

2013 Bodega Applied Phylogenetics Workshop


Phylogenetic methods have revolutionized modern systematics and become indispensable tools in evolution, ecology and comparative biology, playing an increasingly important role in analyses of biological data at levels of organization ranging from molecules to ecological communities. The estimation of phylogenetic trees is now a formalized statistical problem with general agreement on the central issues and questions. A nearly standard set of topics is now taught as part of the curriculum at many colleges and universities. On the other hand, application of phylogenetic methods to novel problems outside systematics is an area of special excitement, innovation, and controversy, and perspectives vary widely.

The course will be held at the Bodega Marine Laboratory on the Northern California coast, which has on-site housing. Our newly increased bandwidth and access to computing clusters allows us to utilize computer-intensive approaches even in a one-week course. The course format will involve equal parts of lecture, discussion, and hands-on software training. One afternoon during the week will be left free for field trips to local natural areas.

Topics Covered

  • Estimating, evaluating and interpreting phylogenetic trees
  • Recent advances in Bayesian and Maximum-likelihood estimation of phylogeny
  • Estimation of species trees, gene-tree/species-tree conflicts
  • Divergence-time estimation from sequence data: relaxed clocks, fossil calibration
  • Analysis of character evolution: maximum likelihood and Bayesian approaches, ancestral-state estimation, character correlation, rates of trait evolution
  • Analysis of morphological form, function of complex character systems
  • Inference of diversification rates: detecting rate shifts, testing key innovation hypotheses
  • Model specification issues: model selection, adequacy and uncertainty
  • Diagnosing MCMC performance

Instructors for the 2013 workshop

  • Jeremy Brown
  • Jonathan Eisen
  • Rich Glor
  • Tracy Heath
  • Mark Holder
  • John Huelsenbeck
  • Luke Mahler
  • Brian Moore
  • Samantha Price
  • Bruce Rannala
  • Bob Thomson
  • Peter Wainwright

Plus special guest lecturers!!


Available housing limits course enrollment to ~30 students. Preference is given to doctoral candidates who are in the early to middle stages of their thesis research, and who have completed sufficient prerequisites (through previous coursework or research experience) to provide some familiarity with phylogenetic methods. Unfortunately, because of limits on class size, postdocs and faculty are discouraged from applying.

Admission and Fees

Students will be admitted based on academic qualifications and appropriateness of research interests. The course fee is $650. This includes room and board at BML for duration of the course (arriving March 2, leaving March 9) and transportation from Davis to BML.

Application Deadline

Applications are due by November 16, 2012. Please send a completed application form and one letter of recommendation from your major advisor. Applications should be sent via email as PDFs to Students will be notified via e-mail by December 1, 2012 of acceptance.


FAQ page with questions.

Send all application materials to:

Gideon Bradburd
Department of Evolution and Ecology
5343 Storer Hall
University of California Davis
Davis, CA

Course Organizers
Brian Moore and Peter Wainwright