fastDFE

fastDFE enables fast and flexible inference of the distribution of fitness effects (DFE) from site-frequency spectrum (SFS) data.

Key Features:

• Joint DFE Inference: Enables efficient joint inference of multiple DFEs that share parameters.
• Genomic Covariates: Supports introduction of genomic covariates that influence DFEs and testing of their significance.
• VCF-to-SFS Parsing: Provides comprehensive utilities for converting VCF files to SFS data with options for site filtering, stratification, site-degeneracy annotation, and probabilistic ancestral-allele inference.
• R Interface: Incorporates a full R interface including native R visualization capabilities.

Scientific Applications:

• DFE Estimation: Estimates the distribution of fitness effects of new mutations for applications in evolutionary biology, ecology, and conservation.
• Covariate Testing: Tests the significance of genomic covariates that influence DFEs.
• Complete DFE Workflow: Covers the entire workflow of DFE inference from raw VCF file acquisition through to analysis.

Methodology:

fastDFE performs inference from site-frequency spectrum data, with VCF-to-SFS parsing utilities that include site filtering, stratification, site-degeneracy annotation, and probabilistic ancestral-allele inference.