SNPGenie

SNPGenie estimates evolutionary parameters from pooled next-generation sequencing (NGS) data to quantify nucleotide diversity, gene diversity, distance from a reference genome, and selection signatures from SNP calling results.

Key Features:

• Input Requirements: Accepts FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with coding sequence (CDS) annotations, and SNP reports in various formats.
• Estimation Capabilities: Computes nucleotide diversity, distance from the reference genome, and gene diversity for specified regions.
• Polymorphism Categorization: Classifies polymorphisms as nonsynonymous, synonymous, or ambiguous.
• Analysis Scales: Performs analyses at single-nucleotide, single-codon, sliding-window, whole-gene, and whole-genome/population levels to detect positive and purifying selection.
• Overlapping Reading Frames: Flags sites with multiple overlapping reading frames for correct interpretation of functional impact.

Scientific Applications:

• Evolutionary biology and population genetics: Quantifies genetic diversity and selection pressures within populations using pooled NGS data.
• Selection detection: Identifies genes or regions under positive or purifying selection via comparative diversity metrics and polymorphism classification.
• Adaptation studies: Investigates the genetic basis and dynamics of adaptation across genomic scales from codons to whole genomes.

Methodology:

Accepts FASTA reference(s), a GTF file containing CDS annotations, and SNP reports in various formats; computes nucleotide diversity, distance from reference, gene diversity, and categorizes variants as nonsynonymous, synonymous, or ambiguous. SNPGenie is implemented in Perl with no additional dependencies.