Workshop: Coordinating Work on Computational Challenges in Phylogenetic Reconstruction

Saturday June 3, 8:30 am to 5:30 pm

2460 AV Williams Bldg.

Coffee and a light breakfast will be available starting at 8:30 am.

Session I: 9:00 - 10:30 am

Focus: New and Emerging Computational Issues

Bernard Moret, "Parallel computing on uniform-memory-access shared-memory architectures: linear speed-ups for complex combinatorial problems" ABSTRACT

Lisa Vawter, "Inclusion of distant taxa"

Discussion Topics

Are exact solutions necessary?

Do genetic algorithms have inherent advantages in a chaotic data space?

Can we develop a distributed, heterogeneous computing network for phylogenetics analogous to the SETI screensaver?

Session II: 11:00 - 12:30 am

Focus: Moving Beyond the Tree

James Rodman, "Broccoli, capers, papayas: Molecular phylogenetics of nouvelle cuisine"

Jungho Lee, "Phylogeny of charophytes - evidence from the chloroplast genome"

Discussion topics

How will phylogenetic research interface and integrate with genomic research?

Are there objective techniques for extracting macromolecular structural and functional information from gene phylogenies?

Lunch will be provided

Session III: 1:30 - 3:00 pm

Focus: Analytical Advances

Bret Larget, "A Bayesian approach to phylogenetic inference from genome arrangement data"

Brent Mishler, "Compartmentalization revisited"

Mark Chase, "Rigorous analyses on single gene matrices do not lead to more correct groups: a perspective based on results from matrices composed of several genes"

Discussion Topics

What are key outstanding analytical issues in phylogenetic reconstruction?

Long branches: what defines them, and how do we deal with them?

Session IV: 3:30 - 5:00 pm

Focus: Information Presentation

Brent Mishler, "The ultimate rank-free database"

See this example of deep green data displayed as a hyperbolic map:

Jessica Kissinger, "Visualizing the Plasmodium and Toxoplasma Genomes"

Junhyong Kim will lead a discussion on data visualization.

Discussion Topics

Are there more efficient ways of displaying phylogenetic information than the commonly used "phylogram"?

Is it possible to develop an integrated system for database management, phylogenetic analysis, and data visualization that can be automated in such a way that a non-expert can extract useful phylogenetic information on demand? And if so, is this our goal?

Session V: 5:00 - 5:30 pm

Closing Discussion

Dinner - 6:30 pm, U.M. Inn and Conference Center

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