PPT-Species Tree Estimation Tandy Warnow

University of Illinois at UrbanaChampaign http tandycsIllinoisedu Orangutan Gorilla Chimpanzee Human From the Tree of the Life Website University of Arizona Species Tree . The Swan Hill fruitless olive tree has quickly gained in popularity. It's attractive foliage and form is enhanced by its absence of fruit, and makes its use in entryways and other high foot-traffic areas a plus. Olives, after all, are best in martinis, on pizza or enjoyed at the table one by one. gutmannhelsinki Dept of Mathematics Statistics Dept of Computer Science and HIIT University of Helsinki aapohyvarinenhelsinki Abstract We present a new estimation principle for parameterized statistical models The idea is to perform nonlinear logist All these partitioned analyses of concatenated data sets make the assumption . t. hat all the genes share a common gene tree.. However there are several important reasons that phylogeny estimates from separate genes might be incongruent.. Phylogenomics. . (Phylogenetic estimation from whole genomes). Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website,. University of Arizona. Species Tree. Large-scale statistical phylogeny estimation. L.L. Knowles et al., Molecular . Phylogenetics. and Evolution 65 (2012): 501-509. Full modeling versus summarizing gene-tree uncertainty: . Method choice and species-tree accuracy. (a) . Estimate. . Tandy Warnow. The University of Illinois at Urbana-Champaign. Brief history. We met in 1992, when I was working in the Discrete Algorithms Group at Sandia National Labs.. I moved to the University of Pennsylvania in 1993, then to the University of Texas at Austin in 1999. No papers yet. Tandy Warnow. Departments of Computer Science and Bioengineering. University of Illinois at Urbana-Champaign. Large-scale statistical phylogeny estimation. Ultra-large multiple-sequence alignment. Estimating species trees from incongruent gene trees. Tandy Warnow. The University of Texas at Austin. Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website,. University of Arizona. Phylogeny. (evolutionary tree). Applications. . of Phylogeny Estimation . Newick strings. Representing rooted trees using clades and rooted triplet trees. Constructing a rooted tree from its set of clades using Hasse Diagrams . Constructing a rooted tree from rooted triplet trees using Aho, Sagiv, Szymanski, and Ullman . Constructing unrooted trees from bipartitions. Compatible binary characters. Constructing trees from compatible binary characters. Introducing . maximum parsimony. Maximum parsimony is not statistically consistent under standard models of sequence evolution!. Tandy Warnow. Departments of Bioengineering and Computer Science. http://. tandy.cs.illinois.edu. Course Details. Office hours: . To be determined. Course webpage: . http://tandy.cs.illinois.edu/598-. species trees . from genome-scale data. Tandy Warnow. The University of Illinois. Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website,. University of Arizona. Phylogeny. (evolutionary tree). All these partitioned analyses of concatenated data sets make the assumption . that all the genes share a common gene tree.. However there are several important reasons that phylogeny estimates from separate genes might be incongruent.. Introducing maximum parsimony. Maximum parsimony is not statistically consistent under standard models of sequence evolution!. Dynamic programming to solve maximum parsimony on a fixed tree. Maximum Parsimony.