$ ./popgenejs --open
Population genetics you can run.
PopGeneJS is a free suite of 40 interactive simulations, from Hardy–Weinberg and genetic drift to selective sweeps, GWAS and low-coverage sequencing. Every module comes with a guided walkthrough, and everything runs in your browser.
popgenejs.bioinformat.org
modules: 40 in 9 categories
walkthroughs: one per module, narrated
runs_in: your browser
install: none
data_uploaded: none
export: CSV, JSON
why it exists
See the forces of evolution at work.
Population genetics is easiest to learn by changing a parameter and watching what happens. PopGeneJS continues the WinPop and PopGene.S teaching software first released in 2005, rebuilt for the web and extended to modern genomics.
Explain walkthroughs on every module
A narrated, step-by-step tour sets the parameters, runs the simulation and points at what to look for. Mechanism animations show what a result chart cannot: gene copies drawn from an urn, a selection sieve, recombination, coalescing lineages, reads piling up.
Nothing to install, nothing uploaded
Every simulation runs in the browser. Students open a link on any laptop, tablet or lab computer; no accounts, no server, no data leaves the machine.
Built for teaching
Theoretical expectations drawn alongside the simulations, help panels with formulas and references, theory pages, and deep links such as ?explain=3 that open a walkthrough at a given step for a lecture or an assignment.
Reproducible results
Save runs in the browser, overlay them to compare parameter settings, and export them as CSV or JSON. The genomics modules are seeded, so a seed and its parameters reproduce a result exactly.
40 modules
From Hardy–Weinberg to genome scans.
Allele & genotype frequencies
3De Finetti diagram, genotype frequencies, chi-square test for HWE
Genetic drift
8Pure drift, drift with selection or mutation, combined forces, Markov chain, heterozygosity loss, bottleneck, founder effect
Natural selection
3Directional, over- and underdominance, dominance, frequency-dependent selection
Mutation
4Two-way and irreversible mutation, neutral mutations, Muller's ratchet
Mating systems
4Autosomal and X-linked loci, assortative mating, the full mating matrix
Gene flow & structure
5Continent–island, island–island, stepping-stone, F-statistics, Wahlund effect
Linkage disequilibrium
3D, D′ and r², the limits of D, decay with recombination
Advanced
2Coalescent and molecular population genetics (θ, π, Tajima's D), quantitative traits
Genomics & NGS
8Low-coverage sequencing, pool-seq, site frequency spectrum, selective sweeps, PCA & admixture, GWAS & stratification, LD decay & Ne, runs of homozygosity
Teaching population genetics?
Use PopGeneJS in your course for free. Get in touch if you need a custom module, an exercise set or a version for your own curriculum.