Dsuite

Dsuite computes Patterson's D (ABBA-BABA) and f4-ratio statistics directly from Variant Call Format (VCF) files to assess gene flow and introgression among populations or closely related species.

Key Features:

• Statistics computed: Calculates Patterson's D (ABBA-BABA) and f4-ratio statistics for testing introgression and gene flow.
• Input format: Operates directly on Variant Call Format (VCF) files without requiring custom input formats.
• Scalability: Performs genome-scale calculations across all possible combinations of tens to hundreds of populations or species.
• Per-locus inference: Determines whether introgression signals are confined to specific loci.
• f-branch method: Implements the f-branch approach to aid interpretation of complex systems of f4-ratio results.
• Implementation: Implemented in C++ for computational efficiency on large datasets.

Scientific Applications:

• Detecting gene flow: Testing for historical or recent gene flow between populations or closely related species using ABBA-BABA and f4-ratio statistics.
• Genome-wide hypothesis testing: Evaluating gene flow hypotheses at genome scale across many taxa.
• Localizing introgression: Identifying loci or genomic regions that show evidence of introgression.
• Interpreting complex signals: Resolving and interpreting complex patterns of f4-ratio results across taxa using the f-branch method.

Methodology:

Computes Patterson's D (ABBA-BABA) and f4-ratio statistics directly from VCF files across all combinations of populations or species and implements the f-branch method; implemented in C++.