Microsatellite Data Checking Software
Micro-Checker is a Windows application that checks for microsatellite null alleles and scoring errors. It also provides null allele estimates, and adjusts allele and genotypes frequencies.

By Cock van Oosterhout, Bill Hutchinson, Derek Wills and Peter Shipley

Genetic studies that utilise archived, archaeological or extracorporeal samples (e.g. hairs, blood, feathers) are often hindered by low template DNA concentrations and/or the presence of polymerase chain reaction (PCR) inhibitors. Where microsatellite loci are specifically targeted, such factors may result in the incorrect assignment of microsatellite genotypes. Genotyping errors may also arise in studies using fresh DNA, where primer-site mutations result in non-amplified alleles (null alleles), and PCR artefacts cause large allele drop-out (i.e. short allele dominance) and stuttering. Such errors can cause deviations from Hardy-Weinberg equilibria, and may bias both spatial and temporal population genetic analyses.

MICRO-CHECKER is a Windows-based software package for Windows 98 SE, 2000 and XP (not yet tested on NT or ME), which can test the genotyping of microsatellite data from diploid populations. The program aids the identification of various genotyping errors, and can also detect typographic errors. MICRO-CHECKER estimates the frequency of null alleles at a locus using a series of algorithms. Importantly, MICRO-CHECKER can also adjust allele and genotype frequencies of the amplified alleles, which allows the data to be used in further population genetic analysis, for instance with GenePop, Arlequin or Fstat.

There are two versions of the Micro-Checker software. The first version is designed to be installed on the computer. If the user is unable to install the program (the user may not have the required administrator rights, for example), a second version is available that can be run directly from the folder where it has been unzipped.


MicroChecker 2.2.3 (Installed Version) – (18.6mb) MicroChecker 2.2.3 (Stand-alone Version) – (19.7mb)

Null allele estimator with inbreeding (Excel)

Related Downloads

Molecular Ecology Notes Paper – PDF (128.3kb)

This is an electronic version of an article published in Molecular Ecology Notes: complete citation information for the final version of the paper, as published in the print edition of Molecular Ecology Notes, is available on the Blackwell Synergy online delivery service, accessible via the journal’s website at or

Estimation and adjustment of microsatellite null alleles in nonequilibrium populations: van Oosterhout et al 2006 MEN