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.