DIMACS Center, CoRE Building, Rutgers University

**Organizer:****Katherine St. John**, The City University of New York, stjohn@lehman.cuny.edu

DIMACS Workshop on Phylogenetic Trees and Rapidly Evolving Diseases, June 21 - 22, 2006.

DIMACS Working Group on Phylogenetic Trees and Rapidly Evolving Diseases II, June 23, 2006.

DIMACS Working Group on Phylogenetic Trees and Rapidly Evolving Diseases I, September 7 - 8, 2004.

Title: Maximum Likelihood inference for phylogenetics

The goal of maximum likelihood phylogenetic inference is to obtain the best tree that describes relationships between extant species. This tutorial will introduce the concepts of both maximum likelihood inference and hypothesis testing. Models of sequence evolution on a tree will be discussed in detail and some of the common models used for DNA and amino acids introduced. Recent extensions to the basic models will be presented.

Title: Parsimony Reconstruction of Phylogenetic Trees

Maximum parsimony and maximum compatibility are two well-known criteria that are used in phylogenetic inference. I will introduce both approaches and discuss some of their connections with discrete mathematics. I will also sketch some applications of compatibility and parsimony to problems such as recombination and supertree construction

Title: Statistical Overview

This session will cover coalescent-based population genetic theory and its application to rapidly evolving pathogens including HIV and Hepatitis C. The focus will be on full probabilistic models that combine population demographic models using the Kingman coalescent with models molecular evolution using the Felsenstein likelihood.

Recommended reading:

- Drummond, A.J., G.K. Nicholls, A.G. Rodrigo & W. Solomon (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161 (3): 1307-20.
- Drummond, A.J., O.G. Pybus, A. Rambaut, R. Forsberg & A.G. Rodrigo (2003) Measurably evolving populations. Trends Ecol Evol 18: 481-488.

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Document last modified on June 13, 2006.