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Statistical tree estimation

Statistical tree estimation

Statistical tree estimation. Tandy Warnow. Topics: March 6-15. Stochastic models of sequence evolution Distance-based estimation Maximum parsimony tree estimation Maximum likelihood tree estimation Bayesian tree estimation. March 6, 2017. Two sequence evolution models:

By lysa
(169 views)

14 Molecular Evolution and Population Genetics

14 Molecular Evolution and Population Genetics

14 Molecular Evolution and Population Genetics . Population Genetics. Gene pool = the complete set of genetic information in all individuals within a population Genotype frequency = proportion of individuals in a population with a specific genotype

By xalvadora
(191 views)

Lecture 3 Molecular Evolution and Phylogeny

Lecture 3 Molecular Evolution and Phylogeny

Lecture 3 Molecular Evolution and Phylogeny. Facts on the molecular basis of life. Every life forms is genome based Genomes evolves There are large numbers of apparently homlogous intra-genomic (paralog) and inter-genomic (ortholog) genes

By fell
(276 views)

Models of Molecular Evolution I

Models of Molecular Evolution I

Models of Molecular Evolution I. Level 3 Molecular Evolution and Bioinformatics Jim Provan. Page and Holmes: Sections 7.1 – 7.2. 1.00. 600. 500. Shark. 0.75. Carp. Fossil divergence time. 400. Frog. Dayhoff distance (to humans). Myr ago. 0.50. 300. Alligator.

By gilda
(92 views)

Population Genetics and Recombination Histories

Population Genetics and Recombination Histories

Population Genetics and Recombination Histories. Finding Minimal Recombination Histories. 1. 2. 3. 4. 1. 2. 3. 1. 4. 2. 3. 4. Population Genetics and Genealogies. Forward in time. Backward in time. NOW. Recombination. Gene Conversion. Coalescent/Duplication. Mutation.

By zuzana
(109 views)

Major Application Areas of Molecular Evolution

Major Application Areas of Molecular Evolution

Major Application Areas of Molecular Evolution. The Role of Models The Assumption of Basic Models The Famous Models: JC69, K80, F81, HKY85, REV,… Finer points: Codons, Heterogeneity, Local Dependency, overlapping constraints, Hidden Structure Dependency, Selection, Testing Models

By gustav
(73 views)

An Introduction to Phylogenetic Methods

An Introduction to Phylogenetic Methods

An Introduction to Phylogenetic Methods. Part one. Dr Laura Emery Laura.Emery@ebi.ac.uk www.ebi.ac.uk /training. Objectives. After this tutorial you should be able to … Discuss a range of methods for phylogenetic inference, their advantages , assumptions and limitations

By vahe
(191 views)

New methods for simultaneous estimation of trees and alignments

New methods for simultaneous estimation of trees and alignments

New methods for simultaneous estimation of trees and alignments. Tandy Warnow The University of Texas at Austin. How did life evolve on earth?. An international effort to understand how life evolved on earth

By astin
(92 views)

New methods for simultaneous estimation of trees and alignments

New methods for simultaneous estimation of trees and alignments

New methods for simultaneous estimation of trees and alignments. Tandy Warnow The University of Texas at Austin. Species phylogeny. From the Tree of the Life Website, University of Arizona. Orangutan. Human. Gorilla. Chimpanzee. How did life evolve on earth?.

By bryce
(62 views)

Phylogenetics

Phylogenetics

Phylogenetics. Motivation Concepts Algorithms. Motivation. Life arose just once - “Thou art my brethren but a few sequences removed”

By barney
(94 views)

Genome Research 2004 By Peter D. Keightly & Toby Johnson

Genome Research 2004 By Peter D. Keightly & Toby Johnson

MCALIGN: Stochastic Alignment of Non-coding DNA Sequences based on an Evolutionary Model of Sequence Evolution. Genome Research 2004 By Peter D. Keightly & Toby Johnson. Majid Kazemian. Motivations.

By karis
(87 views)

MCALIGN Monte Carlo Align A sequence evolution model based alignment method

MCALIGN Monte Carlo Align A sequence evolution model based alignment method

MCALIGN Monte Carlo Align A sequence evolution model based alignment method Keightley PD, Johnson T ., MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution, Genome Res. 2004 Mar;14(3):442-50. Non-coding DNA and heuristics.

By dustin-cotton
(59 views)

Doug Szajda Mike Pohl * Jason Owen Barry Lawson

Doug Szajda Mike Pohl * Jason Owen Barry Lawson

Toward a Practical Data Privacy Scheme for a Distributed Implementation of the Smith-Waterman Genome Sequence Comparison Algorithm. Doug Szajda Mike Pohl * Jason Owen Barry Lawson. 1. Large-Scale Distributed Computations. Easily parallelizable, compute intensive

By edan-charles
(73 views)

New methods for simultaneous estimation of trees and alignments

New methods for simultaneous estimation of trees and alignments

New methods for simultaneous estimation of trees and alignments. Tandy Warnow The University of Texas at Austin. Species phylogeny. From the Tree of the Life Website, University of Arizona. Orangutan. Human. Gorilla. Chimpanzee. How did life evolve on earth?.

By nicole-bentley
(42 views)

Introduction to Phylogenetic Estimation Algorithms

Introduction to Phylogenetic Estimation Algorithms

Introduction to Phylogenetic Estimation Algorithms. Tandy Warnow. Phylogeny. From the Tree of the Life Website, University of Arizona. Orangutan. Human. Gorilla. Chimpanzee. Phylogenetic Analysis. Gather data Align sequences Estimate phylogeny on the multiple alignment

By ramona-cummings
(155 views)

New methods for simultaneous estimation of trees and alignments

New methods for simultaneous estimation of trees and alignments

New methods for simultaneous estimation of trees and alignments. Tandy Warnow The University of Texas at Austin. How did life evolve on earth?. An international effort to understand how life evolved on earth

By maverick-robertson
(43 views)

New methods for simultaneous estimation of trees and alignments

New methods for simultaneous estimation of trees and alignments

New methods for simultaneous estimation of trees and alignments. Tandy Warnow The University of Texas at Austin. Species phylogeny. From the Tree of the Life Website, University of Arizona. Orangutan. Human. Gorilla. Chimpanzee. How did life evolve on earth?.

By daniel-watkins
(61 views)

GSR The Gene Sequence evolution model with iid Rate variation over tree

GSR The Gene Sequence evolution model with iid Rate variation over tree

GSR The Gene Sequence evolution model with iid Rate variation over tree. Örjan Åkerborg, KTH Lars Arvestad, KTH Jens Lagergren, KTH Bengt Sennblad. What?. Gene evolution through duplication and loss Sequence evolution. Why?. Base reconciliation analysis directly on data

By quinlan-gregory
(82 views)

Comparing Two Protein Sequences

Comparing Two Protein Sequences

Comparing Two Protein Sequences. Cédric Notredame. Our Scope. Look once Under the Hood. Pairwise Alignment methods are LIMITED. If You Understand the LIMITS they Become VERY POWERFUL. Pairwise Alignment methods are POWERFUL. Outline. -WHY Does It Make Sense To Compare Sequences.

By lleach
(2 views)


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