Computer Labs

I will post relevant data sets here by Wednesday of the respective week

Lab 1 - genotyping error and data checking

Software Microchecker: Manual, Paper

Software Pedant: Manual, Paper, Poster

Lab Handout, Lecture Slides

Data: A sample of 96 brown rockfish from Point Heyer, Vashon Island, scored at 4 microsatellite loci.

Lab 2 - Statistical tests

Lab Handout , lab handout revised



The two Excel files are only there for your entertainment - you only need the four input files below

Lab 3 - Estimation of population differentiation: FST, AMOVA, genetic distances

Lab Handout



Lab 4 - Power analysis and correction for multiple tests

Lab Handout


POWSIM - make sure you got the newest version (should be dates 12/1/2006)

Excel Spreadsheet - save to your computer. PopTools version of the same




Lab 5 - Relatedness - compressed file with lab handout, data files and spreadsheet


Likelihood based inference of parentage using co-dominant markers. Includes powerful simulations allowing for genotyping error. Original version was published in 1998, but this is a new version (2006) that removed some of the earlier problems. The website provides a brief overview of the basic methods in the program, while the Help file is a more in depth description - both are very good
Java application that does many analyses previously only available in KINSHIP on the Mac platform. Primarily used for pedigree relationship reconstruction and kin group assignments using genetic markers

Lab 6 - Effective population size

Lab Handout

Spreadsheet with data: Ne.xls

Input file for Bottleneck: Forks3BY.txt

input files for Ne-estimator: ForksNe99.txt, ForksNe02.txt, ForksNe05.txt


Ne Estimator
Uses various methods to estimate effective population size. Can be integrated with three other programs, TM3 (Bayesian), McLeeps (multilocus maximum likelihood) and a method allowing immigration (MLNE).
Program to detect recent population bottlenecks from genetic data

Lab 7 - Assignment methods
contains lab handout, Excel sheet of data, input files for GeneClass and Structure and the paper on Forks Creek Assignment by yours truly.

Lab 8 - Landscape Genetics

Lab Handout

Excel spreadsheet with data

Background to the data:

The Tumut fragmentation study

Paper: Peakall et a. 2003

Lab 9 - Selection

FDist2 - download

input files: all years, 2002, 2003, 2004

Lab 10 - Thanksgiving

Lab 11 - Phylogeography

Lab Handout data files for Mega, DNASP and Automated Nested Clade Analysis.

Originating paper: Piertney et al. 2005