Population FST

Compute heterozygosity-based FST from population allele frequencies and explicit weights.

Description

Heterozygosity-based FST summarizes differentiation among populations.

Heterozygosity-based FST summarizes differentiation among populations. A weighted pooled allele frequency provides the total heterozygosity baseline.

Compute heterozygosity-based FST from population allele frequencies and explicit weights.

When to use Population FST

Use this for the following task: Compute heterozygosity-based FST from population allele frequencies and explicit weights.

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.

How to use Population FST and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter alleleFrequencies, populationWeights using the field table, then run the tool.
Read totalHeterozygosity, withinHeterozygosity, fst. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
alleleFrequencies	Allele frequencies	list of number; each entry: number	Required
populationWeights	Population weights	list of number; each entry: number	Required

Pair allele frequencies in [0,1] with nonnegative weights whose sum is positive. Normalize weights, compute both heterozygosities and require HT positive.^[1]

HT=2p̄(1−p̄); HS=weighted mean of 2p(1−p); FST=max(0,(HT−HS)/HT)

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
totalHeterozygosity	Total heterozygosity	number
withinHeterozygosity	Within heterozygosity	number
fst	Fst	number

json

{
  "input": {
    "alleleFrequencies": [
      0.2,
      0.8
    ],
    "populationWeights": [
      1,
      1
    ]
  },
  "output": {
    "totalHeterozygosity": 0.5,
    "withinHeterozygosity": 0.32,
    "fst": 0.36
  }
}

Limitations and assumptions

This is a simple heterozygosity estimator, not a sample-size-corrected Weir–Cockerham estimate.

The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose Island Model Gene Flow for this operation: Estimate Nm from FST under the equilibrium diploid island model, not a direct migration measurement. For a complementary task, use Hardy Weinberg Assumption Audit for this operation: Audit caller-assessed Hardy–Weinberg assumptions without testing observed genotype equilibrium.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Population FST — tool.io

Similar or alternative tools

Island Model Gene Flow
Estimate Nm from FST under the equilibrium diploid island model, not a direct migration measurement.
Hardy Weinberg Assumption Audit
Audit caller-assessed Hardy–Weinberg assumptions without testing observed genotype equilibrium.