MKT

MKT implements the McDonald-Kreitman Test to detect and quantify natural selection by comparing polymorphism and divergence at synonymous and nonsynonymous sites.

Key Features:

• Standard MKT Interface: Analyzes multiple site types within a coding region to detect and contrast synonymous and nonsynonymous changes.
• Advanced MKT Interface: Compares two closely linked genomic regions, coding or noncoding, to discern differential selection pressures between them.
• Multi-Locus MKT Interface: Performs a single multi-locus test across multiple separate loci to assess selection across broader genomic landscapes.
• Generalized MKT approaches: Extends the traditional MKT beyond synonymous/nonsynonymous comparisons to accommodate diverse site classes and genomic contexts.

Scientific Applications:

• Population-genetic inference in Drosophila: Used to demonstrate that selection efficiency correlates positively with effective population size in the Drosophila genus.
• Database annotation (DPDB): Contributes estimates of natural selection to resources such as DPDB to support comparative and evolutionary analyses.

Methodology:

Implements standard and generalized McDonald-Kreitman Test frameworks to compare polymorphism and divergence at synonymous and nonsynonymous sites, to compare closely linked coding or noncoding regions, and to aggregate results across multiple loci.