Hi, Everyone! Hope all is well! Here is a brief overview of the topics that we covered, with a few questions geared to help students study for the upcoming Bioinformatics exam. I will provide you with a few questions for this exam next week. Students are welcome to come by FRIDAY AFTERNOON (tomorrow) to pick up their homeowork assignments, or to ask/discuss questions. I'll distribute the leftovers in class next Tuesday. Some of you have been coming in regularly for help/advice on your projects, and others I have not seen at all. Please --- make an appointment to come in to see me, especially if your topic is evolutionary and I have not seen you in more than three weeks. Best, Claude dePamphilis Our material on phylogenetics in bioinformatics was roughly divided into five "units", with the greatest time spent in parts 2, 3, and 4. Some of the topics that you should especially focus on, with one or a few goals or questions follow each section. 1. concepts of trees and inferences based on trees - trees as hypotheses of evolutionary history and shared ancestory - HOMOPLASY: convergence, parallelism, reversal - gene trees I: orthology, paralogy - monophyly - inference of ancestral states using ACCTRAN * be able to "read" a phylogenetic tree, and draw correct inferences about the monophyly of groups of organisms or sequences * given a tree and a set of data for a given character, be able to infer the ancestral states of the character using the method of ACCTRAN 2. methods of building phylogenetic trees - parsimony, distance, likelihood compared and contrasted - the basic approaches, similarities and differences - standard (nonparametric) bootstrap in phylogenies: use and interpretation - strengths and weaknesses of each of the major methods - PHYLIP as an intro to computer programs for phylogeny * be able to perform and interpret a small parsimony analysis by hand, as we did in class, or using any of the main approaches including boostrap, with PHYLIP 3. distance models of sequence evolution * contrast the different distance models for sequence (or protein) evolution. What are some advantages and disadvantages? 4. maximum likelihood as a general tool for hypothesis testing * what is the likelihood ratio test and how is it used to test a wide variety of possible hypotheses about sequence evolution, such as: rates of evolution, monophyly of group or sequences, similarity of branching history of two trees, etc. * be able to outline or diagram the goals and basic steps in a parametric bootstrap analysis, and it's use in hypothesis testing in sequence studies. 5. further concepts and their application - gene families II, reconciled gene trees - simulation studies of phylogenetic trees: - long branch attraction conditions, causes - summary of my approaches to finding "good trees" * your homework was a good example of phylogenetic analyses where different methods gave different results, but the different results led to a better understanding of the history of the sequences. What were some "take home lessons" to be gained from this exercise?