'Branch lengths' presentation slideshows

Brief Introduction to the Theory of Evolution

Brief Introduction to the Theory of Evolution. Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence Analysis gorm@cbs.dtu.dk. Classification: Linnaeus. Carl Linnaeus 1707-1778. Classification: Linnaeus. Hierarchical system Kingdom Phylum Class Order

791 views • 65 slides

Advances and Limitations of Maximum Likelihood Phylogenetics

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Visualizing Evolution in Space and Time

775 views • 57 slides

Introduction to Phylogenies

617 views • 47 slides

Maximum Likelihood

Maximum Likelihood. Likelihood The likelihood is the probability of the data given the model. Likelihood. If we flip a coin and get a head and we think the coin is unbiased, then the probability of observing this head is 0.5.

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Phylogenetic methods

C. E. N. T. E. R. F. O. R. I. N. T. E. G. R. A. T. I. V. E. B. I. O. I. N. F. O. R. M. A. T. I. C. S. V. U. Introduction to bioinformatics 2008 Lecture 12. Phylogenetic methods. Tree distances. Evolutionary (sequence distance) = sequence dissimilarity. 5.

535 views • 40 slides

Phylogenetic Tree Reconstruction

I519 Introduction to Bioinformatics, 2012. Phylogenetic Tree Reconstruction. Evolution theory. Speciation Evolution of new organisms is driven by Mutations The DNA sequence can be changed due to single base changes, deletion/insertion of DNA segments, etc. Selection bias

962 views • 40 slides

Introduction to molecular dating methods

Introduction to molecular dating methods. 70. 80. 90. 50. 60. 30. 20. 10. 40. Principles. Ultrametricity: All descendants of any node are equidistant from that node For extant species, branches, in units of time, are ultrametric. A. B. C. D. E. F. 100.

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Chapter 11 Phylogenetic Tree Construction Methods and Programs

Chapter 11 Phylogenetic Tree Construction Methods and Programs. Character based methods Molecular sequences from individual taxa Characters at corresponding positions in alignments are homologous Characters of common ancestor can be traced Each character evolved independently

557 views • 31 slides

Genome evolution: a sequence-centric approach

Genome evolution: a sequence-centric approach. Lecture 10: Selection in protein coding genes. (Probability, Calculus/Matrix theory, some graph theory, some statistics). Tree of life Genome Size Elements of genome structure Elements of genomic information. Simple Tree Models

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The Genome Access Course Phylogenetic Analysis

477 views • 26 slides

Correlated trait evolution

Correlated trait evolution. Maximum likelihood approach (Pagel and Milligan). Procedure. Estimate the set of rates in the q-matrix that maximize the likelihood of the data and calculate that likelihood

335 views • 25 slides

Maximum likelihood (cont.)

Maximum likelihood (cont.). The maximum likelihood criterion. The optimal tree is that which would be most likely to give rise to the observed data (under a given model of evolution). Stepwise view. Propose a tree with branch lengths Consider the first character

395 views • 24 slides

Fixations along phylogenetic lineages

Fixations along phylogenetic lineages. Phylogenetic reconstruction: a simplification of the evolutionary process. Cladists and pheneticists. Anatomy of a phylogenetic tree. Edges and nodes. Depictions of phylogenetic trees. Slanted Cladogram. Rectangular Cladogram. Phylogram. Circle tree.

215 views • 21 slides

Comp. Genomics

Comp. Genomics. Recitation 5 2/4/09 ML in Phylogeny. Based on Slides by Ron Shamir and Nir Friedman. Outline. Maximum likelihood (ML) ML in phylogeny Ancestral sequence reconstruction using ML. Maximum likelihood. One of the methods for parameter estimation

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Hickory Dickory Dock: Understanding the Molecular Clock

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Hickory Dickory Dock: Understanding the Molecular Clock

336 views • 18 slides

Introduction to Bioinformatics

Introduction to Bioinformatics. Phylogenetics Part II Distance-Based Methods. Distance Matrix . (Evolutionary) Distance Many possible measures Fraction of sites that differ between two sequences

582 views • 14 slides

Julie D.Thompson, Desmond G.Higgins and Toby J.Gibson

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Julie D.Thompson, Desmond G.Higgins and Toby J.Gibson. Nucleic Acids Research, 1994, Vol. 22, No. 22, pp. 4673-4680.

235 views • 10 slides

PC1

121 views • 2 slides