'Perfect phylogeny' presentation slideshows

The Population Haplotyping problem

The Population Haplotyping problem. NOTATION : each SNP only two values in a population ( bio ). Call them 0 and 1 . Also , call * the fact that a site is heterozygous. HAPLOTYPE : string over 0, 1 GENOTYPE : string over 0, 1, *

2.33k views • 222 slides

The Population Haplotyping problem

The Population Haplotyping problem. NOTATION : each SNP only two values in a population ( bio ). Call them 0 and 1 . Also , call * the fact that a site is heterozygous. HAPLOTYPE : string over 0, 1 GENOTYPE : string over 0, 1, *

2.29k views • 222 slides

Algorithms for estimating and reconstructing recombination in populations

1.17k views • 107 slides

Reconstructing Ancestral Recombination Graphs - or Phylogenetic Networks with Recombination

Reconstructing Ancestral Recombination Graphs - or Phylogenetic Networks with Recombination. Dan Gusfield UC Davis. Different parts of this work are joint with Satish Eddhu, Charles Langley, Dean Hickerson, Yun Song, Yufeng Wu. Reconstructing the Evolution of Binary Bio-Sequences.

1.08k views • 93 slides

Combinatorial Optimization and Combinatorial Structure in Computational Biology

Combinatorial Optimization and Combinatorial Structure in Computational Biology. Dan Gusfield, Computer Science, UC Davis. Extended Perfect Phylogeny Problems and Applications using. Trees Cycles Chordal Graphs Matroids Networks Bi-Convex graphs Connected components.

884 views • 72 slides

Combinatorial Optimization and Combinatorial Structure in Computational Biology

Combinatorial Optimization and Combinatorial Structure in Computational Biology. Dan Gusfield, Computer Science, UC Davis. Extended Perfect Phylogeny Problems and Applications using. Trees Cycles Chordal Graphs Matroids Networks Bi-Convex graphs Connected components.

729 views • 72 slides

Optimal Phylogenetic Networks with Constrained and Unconstrained Recombination

Optimal Phylogenetic Networks with Constrained and Unconstrained Recombination. Dan Gusfield UC Davis. Different parts of this work are joint with Satish Eddhu, Charles Langley, Dean Hickerson, Yufeng Wu. Reconstructing the Evolution of Binary Bio-Sequences. Perfect Phylogeny (tree) model

659 views • 65 slides

CS 394C September 16, 2013

CS 394C September 16, 2013. Tandy Warnow Department of Computer Sciences University of Texas at Austin. Phylogeny. From the Tree of the Life Website, University of Arizona. Orangutan. Human. Gorilla. Chimpanzee. Phylogeny Problem. U. V. W. X. Y. AGGGCAT. TAGCCCA. TAGACTT.

754 views • 63 slides

Haplotyping via Perfect Phylogeny: A Direct Approach

668 views • 57 slides

L6: Haplotype phasing

982 views • 57 slides

Combinatorial and graph-theoretic problems in evolutionary tree reconstruction

Combinatorial and graph-theoretic problems in evolutionary tree reconstruction. Tandy Warnow Department of Computer Sciences University of Texas at Austin. Phylogeny. From the Tree of the Life Website, University of Arizona. Orangutan. Human. Gorilla. Chimpanzee.

608 views • 52 slides

Multi-State Perfect Phylogeny with Missing and Removable Data: Solutions via Chordal Graph Theory

Multi-State Perfect Phylogeny with Missing and Removable Data: Solutions via Chordal Graph Theory. Dan Gusfield Recomb09, May 2009. The Perfect Phylogeny Model for binary sequences. Only one mutation per site allowed (infinite sites). sites. 12345.

583 views • 48 slides

Phylogenetic Tree

Phylogenetic Tree. Phylogenetic Tree: What it is. Drawing evolutionary tree from characteristics of organisms or some measured distances between them Represented as a tree where nodes are the organisms/objects and arcs are the proximity between the respective nodes

673 views • 40 slides

Phylogenetic Tree

Phylogenetic Tree. Phylogenetic Tree: What it is. Drawing evolutionary tree from characteristics of organisms or some measured distances between them Represented as a tree where nodes are the organisms/objects and arcs are the proximity between the respective nodes

975 views • 40 slides

Chordal Graphs and Evolutionary Trees

Chordal Graphs and Evolutionary Trees. Tandy Warnow. Possible Indo-European tree (Ringe, Warnow and Taylor 2000). Phylogenies of Languages.

401 views • 39 slides

Progress in Combinatorial Haplotyping

333 views • 33 slides

Combinatorial methods in Bioinformatics: the haplotyping problem

467 views • 30 slides

Yun S. Song, Yufeng Wu and Dan Gusfield University of California, Davis

Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombnation Event. Yun S. Song, Yufeng Wu and Dan Gusfield University of California, Davis. Haplotyping Problem. Diploid organisms have two copies of (not identical) chromosomes.

458 views • 30 slides

Perfect Phylogeny MLE for Phylogeny Lecture 14

Perfect Phylogeny MLE for Phylogeny Lecture 14. Based on: Setubal&Meidanis 6.2, Durbin et. Al. 8.1. Final Exam Details. The Final Exam will take Place on Thursday, 3.2.04, 0900, at Taub 4.

452 views • 29 slides

Phylogenetic Trees: Assumptions

345 views • 15 slides