Computer Labs

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

Lab 1 - genotyping error and data checking

Software Pedant: Manual, Paper, Poster

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

GENEPOP: stand-alone program, web based version (usually an older version) manual.
FSTAT:has an extensive help file that explains methods
ChiFish: Comes with manual, but have a look at Ryman & Jorde 2001 for a description of the two approaches.

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

Sock02.xls: Excel spreadsheet with microsatellite and SNP data for four sockeye populations.
Sock02all.xls: The same data in an Excel spreadsheet with Microsatellite Toolkit run already, that is, all the input files are in here.
S02mic: Microsatellite input file for Genepop
S02SNP: SNP input file for Genepop
SNPs.dat: SNP input file for FSTAT
Micros.dat: Microsatellite input file for FSTAT

FSTAT: has an extensive help file that explains methods
Arlequin: general purpose program, but here used for AMOVAs (Analysis of Molecular Variance)
SPSS: general statistics software

Sock0203: same sockeye data as above, but for two years (2002, 2003). Prepare your own input files.

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

CERVUS: 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
KINGROUP: 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

Spreadsheet with data: Ne.xls

Input file for Bottleneck: Forks3BY.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).
Bottleneck: Program to detect recent population bottlenecks from genetic data

Lab7Ass.zip: contains lab handout, Excel sheet of data, input files for GeneClass and Structure and the paper on Forks Creek Assignment by yours truly.