The Allele Frequency Calculator determines the frequency of each allele in a population from observed genotype counts using the direct counting method. Provides the foundation for Hardy-Weinberg analysis, genetic drift modeling, and population genetics research across diploid organisms.
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The calculator for allele frequency determines the proportion of each allele at a genetic locus from observed genotype counts in a population sample. Allele frequency is the most fundamental parameter in population genetics — the starting point for Hardy-Weinberg equilibrium testing, natural selection analysis, genetic drift modeling, and conservation genetics assessment.
For a diploid locus with two alleles (A and a) and genotype counts AA = n₁, Aa = n₂, aa = n₃:
Each homozygous AA individual contributes 2 copies of A; each heterozygous Aa individual contributes 1 copy of each allele. The direct counting method is exact and requires no assumptions about mating patterns or selection. The Hardy-Weinberg equilibrium calculator uses these allele frequencies to test whether observed genotype frequencies match neutral expectations.
Allele frequencies are the currency of evolution. The four evolutionary forces all act by changing them over time:
The Fst calculator quantifies genetic differentiation between populations based on allele frequency differences. Use this online calculator for any diploid population sample.
Under Hardy-Weinberg conditions (random mating, no selection, no mutation, no drift, no migration), genotype frequencies are predicted from allele frequencies: AA = p², Aa = 2pq, aa = q². Significant deviation using a chi-square test indicates at least one evolutionary force is acting on the locus. Common departures include inbreeding (excess homozygotes), natural selection (deficit of a specific genotype), or population stratification. The genotype frequency calculator and population genetics calculators provide the complete analysis toolkit.
Allele frequency monitoring is central to conservation genetics. Endangered populations show characteristic patterns including loss of rare alleles, increased allele frequency variance, and elevated inbreeding coefficients — all detectable through serial allele frequency surveys. Populations below approximately 500–5,000 individuals are at significant risk of allele loss through drift. The effective population size calculator quantifies the rate of drift-driven allele frequency change from demographic data.
Allele frequencies are calculated by counting alleles directly from genotype data:
p = (2 × AA + Aa) / (2 × Total)
q = (2 × aa + Aa) / (2 × Total)
Or equivalently, q = 1 − p. Each homozygous individual contributes 2 copies of one allele, while each heterozygote contributes 1 copy of each allele. The total number of alleles is 2N (where N is the number of diploid individuals).
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In 100 individuals with 50 AA, 40 Aa, and 10 aa: the A allele frequency is (100+40)/200 = 0.70, and the a allele frequency is 0.30.
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With 12 AA, 18 Aa, and 20 aa out of 50 individuals, the A allele frequency is 0.42 and a is 0.58. The recessive allele is more common in this population.
Allele counting uses genotype data directly, which gives exact allele frequencies without any assumptions about dominance or Hardy-Weinberg equilibrium. Phenotype-based methods (like estimating q from the square root of recessive phenotype frequency) assume Hardy-Weinberg equilibrium, which may not hold.
As a rule of thumb, sample at least 30 individuals (60 alleles) for common alleles. For rare alleles (frequency below 5%), much larger samples of 100-500 individuals are needed. The standard error of allele frequency decreases as √(2N), so quadrupling the sample size halves the error.
Yes. Allele frequencies change due to natural selection, genetic drift, mutation, migration, and non-random mating. Tracking allele frequency changes over generations is the fundamental way to study evolution. Only under Hardy-Weinberg conditions do frequencies remain constant.
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