'Unweighted pair group method' presentation slideshows

Phylogeny Reconstruction

Phylogeny Reconstruction. Maureen E Stolzer 03510/03710 Lecture Carnegie Mellon University March 18, 2008. Modified from www.bioalgorithms.info. Outline. Phylogenetics Evolutionary Tree Reconstruction Distance Based Phylogeny Additive and Ultrametric Matrices Neighbor Joining Algorithm

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Phylogenetic Tree Construction

Phylogenetic Tree Construction. Dong Xu Computer Science Department 271C Life Sciences Center 1201 East Rollins Road University of Missouri-Columbia Columbia, MO 65211-2060 E-mail: xudong@missouri.edu 573-882-7064 (O) http://digbio.missouri.edu. Outline. Evolution theory

4.08k views • 69 slides

Introduction to Machine Learning BMI/IBGP 730

Introduction to Machine Learning BMI/IBGP 730 . Kun Huang Department of Biomedical Informatics The Ohio State University. Machine Learning Statistical learning Artificial intelligence Pattern recognition Data mining. Machine Learning Supervised Unsupervised Semi-supervised

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Lecture 1: Overview of Phylogenetic methods and applications

Lecture 1: Overview of Phylogenetic methods and applications. Allan Wilson. Charles Darwin and Alfred Russel Wallace Evolution as descent with modification, implying relationships between organisms by unbroken genetic lines Phylogenetics seeks to determine these genetic relationships.

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Clustering methods used in microarray data analysis

Clustering methods used in microarray data analysis. Steve Horvath Human Genetics and Biostatistics UCLA Acknowledgement: based in part on lecture notes from Darlene Goldstein web site: http://ludwig-sun2.unil.ch/~darlene/. Contents. Background clustering k-means clustering

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CS 177 Phylogenetics II

CS 177 Phylogenetics II. Tree building methods: some examples Assessing phylogenetic data Popular phylogenetic software packages. Tree building methods: some examples Assessing phylogenetic data Popular phylogenetic packages. Phylogenetics II. Disclaimers.

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Phylogenetic Methods

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Clustering

Clustering. Petter Mostad. Clustering vs. class prediction. Class prediction: A learning set of objects with known classes Goal: put new objects into existing classes Also called: Supervised learning, or classification Clustering: No learning set, no given classes

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Phylogenetic Methods

Phylogenetic Methods. Understanding Trees Alignments Distances Clustering Methods Bootstrapping Likelihood Methods Parsimony. Phylogeny of Mammals a good example where molecular sequences have led to a big improvement of our understanding of evolution. Cao et al. (2000) Gene.

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Phylogenetic tree construction

Phylogenetic tree construction. Mai Nakadachi. http://libguides.scu.edu/evolution. Outline. Phylogenetic tree types Distance Matrix method UPGMA Neighbor joining Character State method Maximum likelihood. Phylogenetic tree?.

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Gene expression and protein pathways

Gene expression and protein pathways. Joel S Bader CuraGen jsbader@curagen.com IPAM 2000 Nov 8. CuraGen Background. Product pipeline Therapeutic proteins Therapeutic antibodies Drug targets Technology High-throughput biology labs Bioinformatics/information-intensive. Outline.

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G53BIO - Bioinformatics Phylogenetic Trees

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Building Phylogenies

Building Phylogenies. Distance-Based Methods. Methods. Distance-based Parsimony Maximum likelihood. a 0 b 6 0 c 7 3 0 d 14 10 9 0 a b c d. 0. 1. 2. 3. 4. 5. 6. 7. 8. Distance Matrices. a. b. c. d. Distance matrix is additive if there is a tree that fits it exactly.

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Overview of Phylogeny

1. 4. 3. 5. 2. 5. 2. 3. 1. 4. Overview of Phylogeny. Edentata (anteaters, sloths, armadillos) . New World monkeys. Old World monkeys. Lagomorpha (rabbits) . humans, gorilla, chimpanzee, orangutan. Triconodonts. Rodentia (mice, rats, squirrels). gibbons. Multituberculata.

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Multiple sequence alignment

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Multivariate Analysis

Multivariate Analysis. Pattern Analysis Finding patterns among objects on which two or more independent variables have been measured Principal Coordinates Analysis (PCO) Principal Components Analysis (PCA) ( Flury 1988 ) Cluster analysis ( Everitt 1992)

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Tree Reconstruction

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Phylogenetic Trees

Phylogenetic Trees. Importance of phylogenetic trees What is the phylogenetic analysis Example of cladistics Assumptions in cladistics Frequently used terms Fundamentals of Phylogenetc models Phylogenetic software. Importance of Phylogenetic Tree.

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Background

Characterization of Salmonella enterica Subtypes by Optical Mapping Colin W Dykes OpGen Inc. 708 Quince Orchard Road, Gaithersburg, MD 20878. Background

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