Tandem2

Tandem2 automates binning of microsatellite (short tandem repeat) allele lengths to align observed fragment sizes with integer repeat-unit lengths for accurate downstream population-genetic and QTL analyses.

Key Features:

• Automated allele binning: Sorts observed allele sizes into discrete classes that correspond to integer numbers of repeat units.
• Rounding to repeat-unit integers: Rounds observed allele lengths to valid integers based on microsatellite repeat-unit periodicity.
• Error reduction: Mitigates miscalls and underestimation of allelic richness caused by manual rounding and fragment-size measurement inaccuracies.
• Alignment with expected periodicity: Aligns observed lengths with expected repeat periodicity to preserve integrity of genetic data.
• High-throughput processing: Facilitates processing of large microsatellite datasets for batch allele binning.
• Measurement considerations: Notes measurement complications such as fluorescent dye variation and GC content that affect allele-size precision.

Scientific Applications:

• Population genetics: Produces more accurate allele classifications used to infer population genetic parameters.
• QTL mapping: Provides discrete allele bins for detection and analysis of quantitative trait loci (QTL).
• Selection scans: Supports identification of selective sweeps through reliable microsatellite allele-length data.
• Microsatellite studies: Enables standardized allele-length datasets for analyses of allelic diversity and evolutionary phenomena.

Methodology:

Performs automated binning by rounding observed allele sizes to integer repeat-unit lengths based on microsatellite periodicity.