PoPoolation2

PoPoolation2 compares allele frequencies of single nucleotide polymorphisms (SNPs) across two or more populations to identify population differentiation and genomic regions associated with adaptation or phenotypic variation.

Key Features:

• Population Comparison: Compares allele frequencies of single nucleotide polymorphisms (SNPs) across two or more populations to detect genetic differences.
• Measures of Differentiation: Implements statistical measures including F(ST), Fisher's exact test, and the Cochran-Mantel-Haenszel test applicable to windows, genes, exons, or individual SNPs.
• Visualization: Produces results that can be visualized using the Integrated Genomics Viewer (IGV).
• Implementation: Implemented in Perl and R.

Scientific Applications:

• Measuring Differentiation: Quantifies genetic differentiation between populations for evolutionary and ecological studies.
• Genome-Wide Association Studies (GWAS): Identifies SNPs with significant frequency differences across populations to support association studies linking variants to traits or diseases.
• Experimental Evolution: Tracks genetic changes over time within and between evolving populations under controlled conditions.

Methodology:

Compares allele frequencies of SNPs across two or more populations and applies F(ST), Fisher's exact test, and the Cochran-Mantel-Haenszel test at scales including windows, genes, exons, or individual SNPs; implemented in Perl and R.