geaR

geaR performs evolutionary and population genetic analyses of whole-genome genotype data stored in Genomic Data Structure (GDS) files within the R programming environment.

Key Features:

• GDS format support: Leverages the Genomic Data Structure (GDS) format for memory- and time-efficient querying of large genotype datasets.
• Modular analysis framework: Implements a modular design to apply multiple evolutionary analyses through unified functions.
• GRange object classes integration: Uses GRange object classes to partition genomic data informed by GFF annotation files.
• Codon selection and window construction: Supports codon selection by position or degeneracy and construction of positional and coordinate genomic windows.
• Genetic diversity metrics: Computes dXY, π, and FST to assess genetic diversity and population structure.
• Admixture and tree analysis: Performs admixture analyses and phylogenetic tree construction.
• Sequence output: Exports sequences from analyzed genomic partitions for downstream analysis.
• Ploidy and allele support: Handles varying sample ploidy levels and multiple observed alleles.
• R integration: Operates within the R programming environment.

Scientific Applications:

• Population genetic diversity analysis: Analyze large-scale genomic datasets to quantify patterns of genetic diversity and structure.
• Phylogenetics and evolutionary history: Investigate evolutionary relationships among populations or species using tree-building methods.
• Selection and gene flow studies: Study effects of natural selection and gene flow on genomic variation using diversity metrics.
• Admixture investigation: Explore admixture events and their impact on population genetic composition.

Methodology:

Partitions genome-wide genotype data using GRange object classes informed by GFF annotation files; queries and processes genotype data in GDS format; performs codon selection by position or degeneracy and constructs positional and coordinate genomic windows; computes dXY, π, and FST; conducts admixture analyses and phylogenetic tree construction; exports sequence data from partitions; and supports varying sample ploidy and multiple observed alleles.