SPADS

SPADS analyzes multilocus DNA sequence data to quantify genetic variability, infer population structure, and produce spatial visualizations for population genetics and phylogeographic studies.

Key Features:

• Summary Statistics Computation: Calculates a range of summary statistics characterizing genetic variability at individual loci and across multiple loci.
• Clustering Algorithms: Implements two clustering algorithms available in locus-by-locus and multilocus formats to identify genetic clusters.
• Data Conversion Capabilities: Supports input file conversions compatible with other population genetics programs.
• Visualization Tools (GDISPAL and GDIVPAL): Provides MATLAB and R functions GDISPAL and GDIVPAL that generate interpolating surfaces based on multilocus distance and diversity indices to visualize spatial patterns of genetic differentiation and diversity.
• Comparative Surface Visualizations: Produces colored surface visualizations to compare different datasets or various diversity and distance measures within the same dataset.

Scientific Applications:

• Multilocus DNA sequence analysis: Analyze complex multilocus DNA sequence datasets to characterize genetic variability.
• Population structure and differentiation: Investigate and visualize genetic structure and differentiation among populations.
• Comparative spatial genetic analyses: Compare genetic diversity patterns across geographical regions or datasets using interpolated surface visualizations.
• Phylogeographic inference: Support phylogeographic studies by providing spatially explicit visualizations of diversity and distance measures to aid interpretation.

Methodology:

Computes summary statistics; implements two clustering algorithms in locus-by-locus and multilocus formats; converts input files for use with other population genetics programs; and uses MATLAB and R functions GDISPAL and GDIVPAL to generate interpolating surfaces from multilocus distance and diversity indices and produce colored surface visualizations for comparison.