GenoType/GenoDive
GenoType and GenoDive are two programs for analysing the genotypic diversity in clonal/asexual organisms. Note that this concerns an older version of GenoDive that has only a small fraction of the features of the new version.
GenoType assigns genotypes to individuals, based on molecular marker data. Possible input data comes from microsatellites, allozymes, AFLP's or RAPD's. GenoType can also handle haploid and polyploid data and has some features to take scoring errors or mutations into account.
GenoDive reads genotypic data and calculates a number of indices of genotypic diversity. It can also perform a bootstrap test to see whether these indices are different for pairs of populations. Finally GenoDive can also test for differentiation between populations in genotypic composition (this is not the same as the test for differences in genetic diversity!!).
RecodeData
RecodeData is a simply utility to recode genetic marker data in such a way that all alleles are population specific. This is handy if you want to calculate the standardized genetic differentiation measure that was suggested by Hedrick (2005, Evolution). RecodeData makes it possible to estimate a standardized measure for other Fst-estimators than Gst (though not Rst), plus that it makes it possible to estimate Gst with correction for sampling bias (Meirmans, 2006).
kMeans
kMeans clustering divides a number of objects into a a priori assigned number (k) of groups in such a way that the among-groups Sum of Squares is maximised. This program can perform the clustering on genetic marker data either based on the allele frequencies or using an Analysis of Molecular Variance. This analysis is also included in GenoDive.
dispatchR
dispatchR is a program to automatically schedule a large number of R-scripts. It automatically scans a designated folder on your Mac and runs all R-scripts that it finds in it, distributing them across all available processor cores. I use this performing a simulations or analyses of a large number of data files. Spatial assignments
Spatial assignment is an R-script for performing an assignment test based on an interpolation of the allele frequencies over space. In principle, the code should work fine, but it is still a little rough around the edges, so carefully study your results to see whether they are reliable and make biological sense.
Introgression
Introgression is a program to simulate the introgression from Genetically Modified Crops into a metapopulation of its wild relative. The process can be simulated either deterministically of stochastically. Parameters that can be set are among others: the rate of introgression, the selection acting on the transgene, the number of populations, the population size, and the extinction rate of populations. Requires Mac OS X 10.3 or higher.