John Carlos Garza - Population Genetic Software

M Ratio

Garza and Williamson (2001) demonstrate how M, the ratio of the number of alleles to range in allele size, for a sample of microsatellite loci can be used to detect reductions in effective population size. Two simple software programs related to this ratio are available for download here.

M_P_Val.exe calculates the value of M for a microsatellite data set. It will then simulate an equilibrium distribution of M, according to the method described in Garza and Williamson (2001), and given assumed values for the three parameters of the two-phase mutation model, and rank the calculated value relative to the equilibrium distribution. Using conventional criteria, there is evidence of a significant reduction in population size if less than 5% of the replicates are below the observed value. The input file consists of the relative allele sizes, simple allele counts and assumed mean values for the three parameters: theta=4*effective population size*mutation rate, p_s=mean percentage of mutations that add or delete only one repeat unit (the program actually uses p_s-1) and delta_g=mean size of larger mutations. The proper format for the input file is described here. In a survey of empirical mutation data from the literature, Garza and Williamson (2001) found p_s=0.88 and delta_g=2.8. Theta will be population specific.

Download M_P_Val.exe here

Critical_M.exe will take the number of individuals sampled, the number of loci for which there is data and the three assumed parameter values for the two-phase mutation model and calculate a critical value, M_c, through simulation as decribed in Garza and Williamson (2001). Ten thousand simulation replicates are performed and the M ratio is calculated for each. These values are ranked and M_c is defined such that only 5% of the simulation values fall below.

Download Critical_M.exe here

Note: These run only on Macintosh OS computers. They are binhexed files and can be extracted using Stuffit, available free from Aladdin . Both were written by Ellen Williamson. You can email Ellen .

Bottleneck

The Bottleneck program implements the method for detection of reduction in effective population size using allele frequency data described in Cornuet and Luikart (1996; Genetics). It uses several statistical tests to detect an excess in observed heterozygosity, relative to that expected from the observed allele number, were the data from loci at mutation-drift equilibrium.

Note: Bottleneck runs with the Windows OS.

Download Bottleneck here

Genetix

Genetix is a package of population genetic programs from the Laboratoire Génome, Populations, Interactions in Montpellier, France. It includes modules that calculate F statistics, genetic distances and measures of linkage disequilibrium. It can also perform Mantel tests and other methods in population genetics.

Note: The Genetix interface is entirely in French and it runs with the Windows OS.

Download Genetix here

GenePop

GenePop is a package of population genetic programs from the Génétique et Environnement group of the Institut des Sciences de l'Evolution in Montpellier, France. It calculates estimates of Fst and other population genetic parameters, and performs exact tests for Hardy-Weinberg equilibrium, population differentiation and genotypic disequilibrium among pairs of loci. It also converts GenePop files to formats used by other population genetic programs

Note: GenePop runs with the Windows OS.

Download GenePop here

Arlequin

Arlequin is a package of population genetic programs from the Laboratoire Génétique et Biométrie at the Université de Genève in Switzerland. It is very versatile package that can analyze many different types of data and perform many different analyses, among them calculation of F statistics, analysis of molecular variance, etc.

Note: Arlequin is available in versions that run with the Windows, Macintosh and Linux OS.

Download Arlequin here

WhichRun

WhichRun is a program from Bodega Marine Lab in California that performs population assignment of individuals based on multilocus genotype data. It calculates a multilocus probability that a specific individual comes from each of a number of source populations with specified allele frequencies.

Note: WhichRun runs with the Windows OS.

Download WhichRun here

More software

These are just a few of my favorite software programs, but there are many others available for population genetic analysis. An extensive list, focusing mainly on phylogeny programs, can be found here .