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Bioinformatics Advance Access originally published online on May 6, 2009
Bioinformatics 2009 25(15):1982-1983; doi:10.1093/bioinformatics/btp303
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

TANDEM: integrating automated allele binning into genetics and genomics workflows

Michael Matschiner * and Walter Salzburger

Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland

* To whom correspondence should be addressed.


  Abstract

Summary: Computer programs for the statistical analysis of microsatellite data use allele length variation to infer, e.g. population genetic parameters, to detect quantitative trait loci or selective sweeps. However, observed allele lengths are usually inaccurate and may deviate from the expected periodicity of repeats. The common practice of rounding to the nearest whole number frequently results in miscalls and underestimations of allelic richness. Manual sorting of allele lengths into discrete classes, a process called binning, is tedious and error-prone. Here, we present a new program for the automated binning of microsatellite allele lengths to overcome these problems and to facilitate high-throughput allele binning.

Availability: www.evolution.unibas.ch/salzburger/software.htm

Contact: michael.matschiner{at}unibas.ch

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on December 11, 2008; revised on April 30, 2009; accepted on May 1, 2009

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