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 . 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. Algorithmic Computational Genomics. Tandy Warnow. Departments of Bioengineering and Computer Science. http://. tandy.cs.illinois.edu. Course Details. Office hours: Mondays 10-11:45 in 3235 Siebel. Course webpage: . Algorithmic Computational Genomics. Tandy Warnow. Departments of Bioengineering and Computer Science. http://. tandy.cs.illinois.edu. Course Details. Office hours: . To be determined. Course webpage: . 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 Illinois at Urbana-Champaign. Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website,. University of Arizona. Phylogeny. (evolutionary tree). DNA Sequence Evolution. 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-. Tandy Warnow. The University of Illinois. Avian . Phylogenomics. Project. G . Zhang, . BGI. . Approx. 50 species, whole genomes. 8000+ genes, . UCEs. MTP Gilbert,. Copenhagen. S. . Mirarab. Md. 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.