haploconfig

haploconfig implements statistical tests of neutrality by analyzing haplotype frequency distributions and the observed number of segregating sites to compute rejection probabilities under the standard coalescent and alternative evolutionary models.

Key Features:

• Haplotype Configuration Test (HCT): Uses the full haplotype frequency distribution to evaluate neutrality.
• Summary statistics: Utilizes the observed number of segregating sites and properties of haplotype frequency distributions as key summary statistics.
• Exact computation for small samples: Employs a derived recursion under the standard coalescent to compute exact rejection probabilities for small sample sizes.
• Simulation-based approximation for larger samples: Uses simulation-based methods to approximate rejection probabilities for larger sample sizes.
• Model flexibility: Supports the standard neutral coalescent with or without recombination, exponential population growth, and island migration models.

Scientific Applications:

• Neutrality testing: Tests hypotheses of neutral evolution versus selection using haplotype frequencies and segregating sites.
• Model evaluation and simulation studies: Evaluates rejection probabilities across simulated alternative evolutionary models.
• Empirical data analysis: Applied to empirical datasets, including studies of Drosophila melanogaster.

Methodology:

Derives a recursion under the standard coalescent to compute the joint distribution of haplotype frequencies and segregating sites and obtain exact rejection probabilities for small samples; uses simulation techniques to approximate rejection probabilities for larger datasets and implements the HCT using full haplotype frequency distributions.