Evolutionary Biology Group

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.
(More Information from the Micro-Checker Help pages)

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

The Micro-Checker program is a collaborative project between the *Department of Biological Sciences and the **Department of Computer Science.

Abstract

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.

MICRO-CHECKER is freeware, and the program, with the accompanying help and example files, can be downloaded from the Molecular Ecology & Fisheries Genetics group at the University of Hull using the link below. We are keen to up-date and expand the programme and thus we ask you to answer a few brief questions concerning the occurrence of null alleles, stutter peaks and large allele drop-out in your study species, before downloading the program.

Click here to download Micro-Checker.


Download the Molecular Ecology Notes Paper PDF document

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 http://www.blackwellpublishing.com/men or http://www.blackwell-synergy.com


Inbreeding Corrected Null Allele Estimator.

Download the Excel spreadsheet. Excel spreadsheet


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