Trees in the Desert 2019


A workshop on ultra-large phylogenetic trees

April 12-14, 2019

Tucson, Arizona






Phylogenetic trees with thousands of species, genes or individuals are now being published regularly, and numerous efforts around the globe are aimed at scaling this up even further. The algorithmic challenges for assembling, evaluating, and applying these large trees remain formidable, however, with plenty of room for novel approaches. We invite graduate students in phylogenetic biology, bioinformatics, mathematics and computer science to join us in a three-day workshop on this topic, supported by a grant from the U.S. National Science Foundation. The goal is to communicate aspects of known approaches to the problem, brainstorm collectively about new ideas, and get our hands dirty with exemplar data sets. The ideal student for this will be a mid- to-late Ph.D. student in one of these fields, with some experience in phylogenetic toolkits, programming and bioinformatics infrastructure (e.g., scripting languages, UNIX shell, etc.). Funds are available to support travel, lodging and meals for students.


Topics will likely include constructing large trees, evaluating their robustness and reliability, and integrating them with various post-phylogenetic analyses. Specific topics will be driven by interests and experience of the participants but may include scalability of conventional tree building methods, alignment-free tree construction, model-selection in large trees, coalescent and gene-tree approaches, missing data and terraces, assembling confidence sets of trees for subsequent study, and scalable inference of tree annotations such as divergence times, ancestral states, etc. Aside from short talks the first day, the format will be almost entirely "hands-on", focusing on developing and testing new ideas and pushing existing ones to their feasibility limits.


The workshop will be held at the University of Arizona's Biosphere 2 facility, located in the foothills of the Santa Catalina Mountains about 30 miles north of Tucson. Tucson proper is flanked on its east and west sides by Saguaro National Park, founded as a reserve for the saguaro cactus that is so emblematic of the Sonoran Desert.  April is an exceptional time to visit southern Arizona, with the spring desert bloom well underway, sunny warm days and cool nights. Biosphere 2 is located in mesquite grassland not far from trailheads for the Arizona Trail and other hikes into the Catalina Mountains.


Confirmed instructors:


Mukul Bansal, University of Connecticut

Mark Holder, University of Kansas

Michelle McMahon, University of Arizona

Emily Jane McTavish, University of California, Merced

Jeff Oliver, University of Arizona

Dan Portik, University of Arizona

Mike Sanderson, University of Arizona (Organizer)

Mike Steel, University of Canterbury

Tandy Warnow, University of Illinois at Urbana-Champaign

John Wiens, University of Arizona

Derrick Zwickl, University of Arizona



Application and financial aid


Class size will be kept small, and funds are available to support graduate student travel, meals and lodging. Please copy and paste the questions below and your answers into an email to Mike Sanderson ( by January 25, 2019, together with a copy of your C.V. Also arrange to have one letter of recommendation from your advisor sent to the same email by the deadline.




1. Name and email address:




2. University, degree program, years in program, name of advisor:




3. Briefly describe your knowledge of phylogenetic methods and experience with phylogenetic software tools:




4. Briefly describe your programming experience, if any




5. How is the question of constructing large phylogenetic trees relevant to your research interests?




6. What specific topics would you like to see discussed at this workshop?