Program Code

Welcome. Please click on a link below for more information on program codes written in the Keller Lab. Go here for code written for internal use by the K/M lab, and go here for hints on the use of R.

GeneEvolve - program written in C++ that quickly and efficiently simulates genome-wide array or sequence data under several population genetic scenarios (e.g., natural selection, assortative mating, cultural effects, stratification, etc.). See the paper here.

GeneEvolve - (abandoned) program written in R; this was the forerunner to the program above. It does not output simulated genomic data, only the phenotypes of different relative classes and was therefore designed to be used to test family/twin models (which are newer version can do as well). It was cited in this paper.

FISHR (Find IBD Shared Haplotypes Rapidly) is a program designed to rapidly and accurately detect identical by descent (IBD) shared haplotypes between individuals that arose from common ancestors many 10s of generations ago (lengths > 1 cM). The program is fast enough to be deployed on samples of 20,000 - 50,000 measured on whole-genome SNP arrays. We will post the github repository soon.

Cascade Model - Code written in old Mx. The Cascade model (described here) is a latent variable model that uses extended twin family data to simultaneously estimate several different environmental and genetic contributors to phenotypic variation.

Bivariate Nuclear Twin Family Model - R script in OpenMx for running a bivariate nuclear twin family model, in this case, on height & IQ. The publication related to this script is here.

Plot Parameter Indeterminacy from Classical Twin Models - Code written in Matlab to plot the possible parameter space for estimates of additive genetic variance, non-additive genetic variance, and shared environmental variance.

 

 

 

 

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