BIOL 464/GEN 535

Population and Quantitative Genetics
Laboratory

Fall 2015

 

 

HOME - SCHEDULE -  LABORATORY - BACKGROUND READING

 

Date Topic Data Program Assignments Due

Aug 19

Lab 1: Probability  ppt pdf

Lab Introduction

Answer Key

Sample lab report

Lab Manual for Week 1



 

Aug 26

Lab 2: Hardy-Weinberg Equilibrium ppt pdf

Answer Key

   

Aug 19 report

Sep 2

Lab 3: Exact Tests and Estimating Genetic Variation ppt pdf

Answer Key

human_ssr.xls

pop_codes.txt

GenAlEx

Arlequin

Aug 26 report

Sep 9

Lab 4: Inbreeding and Kinship ppt pdf

Answer Key

pmugo_allozymes.xls


Sep 2 Report

Sep 16

Lab 5: Selection ppt pdf

Answer Key


Populus

Sep 9 Report

Sep 23

Exam 1    

 Sep 16 report

Sep 30

Lab 6: Genetic Drift and Effective Population Size ppt pdf


Answer Key

Mid-Semester Survey

 

Drift Simulation Excel File

Instructions

 


Oct 7

Lab 7: Estimating Population Structure ppt pdf

Answer Key

human_struc.xls

human_by_region.xls

AlleleA1

Structure

structureHarvester.py

Sep 30 report


Oct 14

Lab 8: Individual Identity and Population Assignment ppt pdf

Answer Key

Structure Results of full dataset (file for StructureHarvester)

Structure Project file (Need to unzip to be loaded in Structure)


OmniPop200.1

 

 

Oct 7 report

Oct 21

Lab 9: Estimating Linkage Disequilibrium ppt pdf

Answer Key

aspen_phyB.arp

arab_phyC.arp

LD_aspen_phyB.xls

LD_arab_phyC.xls

human_LD.arp

Haplotype Inference by EM

Oct 14 report

Oct 28

Exam 2      

Nov 4

Lab 10: Mutation ppt pdf

Answer Key


Fisher's Exact Test Calculator

Oct 21 report

Nov 11

Lab 11: Detecting Departures from Neutrality ppt pdf

Wang et al. (1999)

Answer Key



aspen_phy.arp

utr_mays.arp

utr_par.arp

exon_mays.arp

exon_par.arp


Nov 4 report


Nov 18

Lab 12: Phylogenetic and Coalescent-Based Analysis ppt pdf

Answer Key

mt_primates.meg

pdha1_human.meg

pg_ex2.fas

pdha1_human_chimp_align.nexus

Mega

Beast

Tracer

FigTree
 

Nov 11 report

Dec 2

Lab 13: Association Genetics ppt pdf

Course Evaluations

Tassel Tutorial Data

Tassel

User Guide

Nov 18 report