PopGene.S2

PopGene.S2 is a free software utility which comes packed with several approachable options to help you study population genetics. It's not complicated to work with.

Installing this program is a speedy and simple task that doesn't require special attention. It adopts a user-friendly interface that consists of a regular window with a plain structure, where you can explore the menu bar with allele and genotype frequencies, mating models, gametic disequilibrium, drift, selection modes, mutation, gene flow and subdivision, along with molecular population genetics.

It's possible to perform a chi-squared test by entering the observed number of individuals for each genotype and then export the results to plain text documents, as well as to generate plots for genotype frequencies and random mating models by applying autosomal or X-type locus.

Moreover, you can generate graphs for assortative matings (positive with or without dominance, negative, or matrix) as well as for the magnitude of the disequilibrium coefficient, calculate gamete frequencies based on the number of each gamete, put together a simple genetic drift, with selection, mutation or both, run the Markov process by inputting the effective population size, and estimate the H decline over time by specifying the effective population size and initial allele frequency along with the number of generations and populations.

PopGene.S2 also lets you plot general or frequency-dependent selection models, irreversible two-way, neutral or Muller's ratchet mutations, in addition to gene flow and subdivision using continent-island, island-island, F-statistics or Wahlund effect models. Information may be imported from FASTA files (.fas, .fasta).

We haven't come across any difficulties in our tests, thanks to the fact that PopGene.S2 didn't hang, crash or display error messages. It had a good response time and low impact on computer performance, using low CPU and RAM. Although it doesn't seem impressive, PopGene.S2 comes equipped with a lot of options to help you better understand population genetics through graphical representations.