PPT-Newer methods for tree building

Parsimony analysis Maximum likelihood Bayesian inference For all 3 Build an unrooted tree on one of these three criteria ignore synapomorphy and symplesiomorphy and pull root out on tree using . CS/. BioE. 598. Tandy Warnow. Alignment Error/Accuracy. SP-FN: percentage of homologies in the true alignment that are *not* recovered. SP-FP: percentage of homologies in the estimated alignment that are false. and. Algorithms . Huffman compression: An . Application of Binary Trees and Priority Queues. CS 102. Encoding and . Compression. Fax Machines. ASCII. Variations on ASCII. min number of bits needed. cost of savings. phylognetic. trees. Read Chapter 5. Building a tree. Aim in building a . phylogenetic. tree is to use a knowledge of the characters of organisms to build a tree that reflects the relationships between them.. Molecular phylogenetic methods 4. 11-10-2011. Maximum likelihood methods. So far we have only considered a single . site (configuration). . The likelihood for all sites is the product of the likelihoods for each site if all the sites evolve independently. . Marketing Campaign. If you have a question, type it here! . Webinar Semantics. Nicole Wise. Holganix. Head of Marketing. Email: Nwise@holganix.com. Phone: 866-56-EARTH . ext. 300. Agenda. Why tree and shrub?. Kai Müller. Tree searching: exhaustive search. branch addition algorithm. Branch. and bound. L. min. =L. (random tree). „search tree“ as in branch addition. at each level, if . L < L. min. . 1. 4. 3. 2. 5. 1. 4. 2. 3. 5. Phylogenetic Trees. Nodes: species. Edges: time of independent evolution. Edge length represents evolution time. AKA genetic distance. Not necessarily chronological time. Tandy . Warnow. Multiple Sequence Alignment (MSA): . another grand challenge. 1. S1 = -AGGCTATCACCTGACCTCCA. S2 = TAG-CTATCAC--GACCGC--. S3 = TAG-CT-------GACCGC--. …. Sn. = -------TCAC--GACCGACA. Increasing molecular evidence indicates that hybridization is far more . common in animals than has traditionally been recognized. . A. B. C. D. Hybridization. A. B. C. D. A. B. C. D. Non-. Introgressed. Phylogenies. Dr Laura Emery . Laura.Emery@ebi.ac.uk. www.ebi.ac.uk. /training. Objectives. After this tutorial you should be able to…. Use essential phylogenetic . terminology . effectively. Discuss aspects of phylogenies and their implications for phylogenetic . Dr. EP de Villiers. Adapted from: http://. viralzone.expasy.org. / . Tree basics. The . Concept of . Phylogenetic Tree. . Trees . Capture Major Events in a Species' Existence . A tree . is composed of Leaves, Branches, and Inner Nodes . and . Metagenomics. Tandy Warnow. The Department of Computer Science. The University of Texas at Austin. The “Tree of Life”. Applications of phylogenies to:. . protein structure and function. . Folks often use the term “reliability” without a very clear definition of what it is. . Methods of assessing performance - Simulation.. . Enormous advantage that a large number of replicates can be examined, and this allows us to account for . Tandy Warnow. Building vs growing. Building: Given unaligned sequences, compute the alignment and the tree.. Growing: Given an alignment and a tree, but also some new sequences. Building a large alignment and tree.