Large-scale phylogenetic reconstruction and the Tree of Life

n this talk, I will review current computational activities aimed at
reconstructing the Tree of Life, the evolutionary history of all living
organisms (an estimated 10-100 million). Researchers and funding agencies
worldwide have put renewed emphasis on the establishment of evolutionary
relationships among living species; such relationships are fundamental to
research in medicine, drug design, agriculture, ecology, and many other
areas.

The CIPRES (Cyber Infrastructure for Phylogenetic Research), which I direct,
was founded to develop the informatics tools required to attempt a
reconstruction of the Tree of Life. I will sketch the goal and current
achievements of CIPRES, comment on future needs, and relate its work to that
of other research efforts in phylogeny. I will then focus on algorithmic
techniques for large-scale reconstruction, both in terms of speed and in
terms of accuracy. In the process, I will discuss novel divide-and-conquer
approaches broadly applicable across all optimization criteria and types of
data and also review progress in using one specific type of data, gene
rearrangements.
Bernard Moret is currently a
professor at U. New Mexico. He is best known for his work on developing
algorithms for phylogenetic tree construction. He is currently leading the
CIPRES project (http://www.phylo.org/index.html
), which has the following aim:

"the goal of the CIPRES project (pronounced Cypress) is to enable
large-scale phylogenetic reconstructions on a scale that will enable
analyses of huge datasets containing hundreds of thousands of biomolecular
sequences. To achieve this goal we have brought together a group of
researchers involved in phylogeny estimation, statistics, and computer
science to create new solutions for the difficult computational problems
that arise in inferring evolutionary relationships. The project has a 5 year
development plan (2003-2008) to create a national computational
infrastructure for the international systematics community. The group is
committed to providing open-source software."