PEAS

PEAS performs analysis of large single nucleotide polymorphism (SNP) datasets for population genetics and molecular phylogenetics.

Key Features:

• Versatile Data Input and Formatting: Supports various SNP input formats and exports input files for STRUCTURE, frappe, Arlequin, Haploview, LDhat, PLINK, EIGENSOFT, PHASE, fastPHASE, MEGA, and PHYLIP.
• Genetic Distance Matrix Calculation: Calculates genetic distance matrices with bootstrapping options for individuals and populations using genome-wide high-density SNP data and exports results compatible with MEGA and PHYLIP.
• STRUCTURE Output Utilization: Computes genetic distances from STRUCTURE outputs and generates MEGA files for reconstruction of component trees.
• Haplotype Sharing Analysis: Performs haplotype sharing analysis based on high-density SNP data to investigate shared genetic variants among samples.

Scientific Applications:

• Population genetics analyses: Analysis of population structure and genetic differentiation using SNP datasets and STRUCTURE-compatible outputs.
• Molecular phylogenetics: Phylogenetic reconstruction and inference of evolutionary relationships using genetic distance matrices and MEGA/PHYLIP-compatible outputs.
• Haplotype sharing studies: Investigation of shared haplotypes and genealogical relationships among individuals or populations.
• Data preparation for downstream tools: Formatting and exporting SNP data for downstream analysis with PLINK, EIGENSOFT, PHASE, fastPHASE, LDhat, Arlequin, Haploview, MEGA, and PHYLIP.

Methodology:

Calculates genetic distance matrices with bootstrapping for individuals and populations, computes genetic distances from STRUCTURE outputs, performs haplotype sharing analysis, and exports formatted files for STRUCTURE, frappe, Arlequin, Haploview, LDhat, PLINK, EIGENSOFT, PHASE, fastPHASE, MEGA, and PHYLIP.