Summer School on Phylogenetic Combinatorics - Lectures M. Steel

When data are in conflict I

Overview of processes that can lead to conflict (lineage sorting, lateral gene transfer, sampling, systematic error).

When data are in conflict II

Maximum parsimony, distance based methods (e.g. neighbor joining/BME), and safety radius concepts. Ways of combining and summarizing conflicting trees (consensus trees, networks) and measuring discordance between trees.

Stochastic approaches to phylogenetic analysis I

Models of character/sequence evolution: Types of models, Felsenstein zone, distance correction and tree reconstruction. Statistical phylogenetic methods for reconstructing trees and ancestral states.

Dealing with partial information - Lassoing a tree

Tree reconstruction from patchy taxon coverage (the Aho algorithm, MRP, decisiveness). Tree reconstruction from partial distance data.

Stochastic approaches to phylogenetic analysis II

Lineage sorting, gene content models, and lateral gene transfer model. Speciation and extinction models and the expected loss of phylogenetic diversity.