A null allele is an allele with the effect of either absence of the gene product at the molecular level, or the absence of function at the phenotypic level. An allele is any one of a number of alternative forms of the same gene (sometimes the term refers to a non-gene sequence) occupying a given locus (position) on a chromosome. ... This stylistic schematic diagram shows a gene in relation to the double helix structure of DNA and to a chromosome (right). ... The phenotype of an individual organism is either its total physical appearance and constitution, or a specific manifestation of a trait, such as size or eye color, that varies between individuals. ...
A nullallele is one that isn't detected except when it occurs homozygously.
The standard method for estimating the frequency of a nullallele is the Estimation-Maximization (EM) Algorithm, which finds those allele frequencies that maximize the probability of the observed results under the assumption of HWE.
(This algorithm, for the case of a nullallele, is available at http://gause.biology.ualberta.ca/jbrzusto/nullele.html) What is left to do is to determine to what extent, even assuming the existence of a nullallele, there is still evidence of disequilibrium.
Nullalleles can be attributed to several phenomena.
Furthermore, stochastic effects of sampling that occurs during mating may change allele frequencies in a way that is very similar to the effect of nullalleles; an excessive frequency of homozygotes causing deviations from Hardy-Weinberg equilibrium expectations.
Since nullalleles are a technical problem and sampling effects that occur during mating are a real biological property of a population, it is often very important to distinguish between them if excess homozygotes are observed.
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