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Genomic Variation Lab
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ECL
290 Winter 2007
Instructors: Holly Ernest, Bernie May and John Eadie |
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Syllabus course objectives (pdf) software websites (pdf) course questions (pdf) Week 1: Introduction to different types of markers Josh Hull, Molly Stephens, and Rachel Schwartz AFLP powerpoint (pdf) Molly Stephens Microsatellite data and analysis (pdf) Josh Hull Week 2: Review of key population genetic concepts Ann T. Chang, Elizabeth Long, Adam Wentzell, and Jennifer Kurushima Handout on key population genetic concepts (pdf) Elizabeth Long Fstats powerpoint (pdf) Elizabeth Long Hardy-Weinberg and linkage disequilibrium powerpoint (pdf) Ann Chang Notes of frequentist, maximum likelihood, and Bayesian statistics (pdf) Jessica Petersen Allele numbers and frequencies powerpoint (pdf) Jennifer Kurushima Genetic Distance powerpoint (pdf) Adam Wentzell Week 3: Getting Started with a data set (Part 1) Renate Eberl and Lindsay Clark Using NTSYS-pc for Principal Coordinate Analysis of dominant data (pdf) Molly Stephens Whichloci powerpoint (pdf) Lindsay Clark Whichloci handout (pdf) Lindsay Clark Microsatellite toolkit and CONVERT handout (pdf) Renate Eberl getting started with a data set powerpoint (pdf) Renate Eberl Week 4: Getting started with a data set: Genepop on the Web and GDA (Part 2) Rachel Simmons and Mandi Finger Robertson, Alan and Hill, William G. 1984. Deviations from Hardy-Weinberg proportions: sampling variances and use in estimation of inbreeding coefficients. Genetics 107:703-718. GDA user's guide (pdf) Weir, B.S. and C. Clark Cockerham 1984. Estimating F-statistics for the Analysis of Population Structure. Evolution 38:1358-1370. Rice, William R. 1989. Analyzing Tables of Statistical Tests. Evolution 43:223-225. |
Week 5: Getting started with the data set: Genepop on the Web and Fstat (Part 3) Andrea Drauch and Joana Fernandes Genepop and Fstat handout (pdf) Andrea Drauch Week 6: Using STRUCTURE Kraig Kraft and Sarah Brown, Jason Sexton STRUCTURE handout (pdf) STRUCTURE powerpoint (pdf) Choosing a K: log likelihood (pdf) delta K and Evano's ad hoc statistic (pdf) Testing STRUCTURE with complex population structures using simulated data handout (pdf) EASYPOP software:http://www.unil.ch/dee/page36926_fr.html Week 7: GENETIX Ann T. Chang, Philip Lavretsky, and Annabelle Kleist GENETIX handout (pdf) GENETIX powerpoint (pdf) Using FCA (Factorial Correspondence Analysis) powerpoint (pdf) Annabelle Kleist Week 8: Geneclass and Assignment testing Geneclass and assignment testing powerpoint (pdf) Catarina Ginja Assignment testing applications (and misapplications) powerpoint (pdf) Catarina Ginja Week 9: Kinship analysis and relatedness Jennifer Kurushima, Beverly Ajie Relatedness powerpoint (pdf) SPAGeDi handout (pdf) ML-Relate handout (pdf) K-coefficients handout (pdf) Week 10: Parentage analysis Mariah Meek and Jessica Petersen Parentage analysis powerpoint (pdf) Mariah Meek and Jessica Petersen CERVUS powerpoint (pdf) Mariah Meek Comparison between CERVUS and ML-Relate powerpoint (pdf) Jessica Petersen CERVUS handout (pdf)
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