Contemporary Challenges in Large-Scale Sequence Alignments and Phylogenies

Bridging Theory and Practice


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With the increased availability of high quality sequence data and fully assembled genomes, the ability to construct large evolutionary trees is now mainly limited by the available mathematical models and computational methods. A key aspect of this workshop is the emphasis on scalable models and methods for phylogeny estimation, both of genes and of species, and for multiple sequence and multiple whole genome alignment, which are necessary precursors to these problems. This workshop will bring together mathematicians, probabilists, statisticians, computer scientists, and biologists at the forefront of these fascinating questions, with the goal of supporting the development of new theoretical advances and estimation methods that can scale to large datasets with high accuracy.

This workshop will include talks focused on theoretical contributions from mathematics and statistics, as well as talks focused on method development and analyses of biological datasets. A final day of the workshop (Thursday, August 14, 2025) will be devoted to a Software School, which will provide demos and tutorials of advanced software for topics discussed in the workshop; this Software School will be aimed at training biologists, from undergrads through postdocs, to use the current leading methods for multiple sequence alignment and phylogenetic estimation. A one-hour tutorial will be provided to introduce the concepts of the talks that will be presented, so that attendees who are relatively new to phylogenetics are able to understand the material.

This workshop will include lightning talks and a poster session for early career researchers (including graduate students). If accepted, you will be asked to do both. In order to propose a lightning session talk and a poster, you must first register for the workshop, and then submit a proposal using the form that will become available on this page after you register. The registration form should not be used to propose a lightning session talk or poster.

The deadline for proposing is June 8, 2025. If your proposal is accepted, you should plan to attend the event in-person.


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Siavash Mirarab University of California, San Diego
Sébastien Roch University of Wisconsin, Madison
Tandy Warnow University of Illinois, Urbana-Champaign