sampletrees

sampletrees performs Markov chain Monte Carlo (MCMC) sampling of gene genealogies from phased or unphased single nucleotide polymorphism (SNP) genotype data to infer evolutionary relationships and demographic history.

Key Features:

• MCMC Sampling: Executes Markov chain Monte Carlo sampling to approximate the posterior distribution of gene genealogies given genetic data.
• Data Compatibility: Operates on both phased and unphased SNP genotype data.
• Implementation: Implemented in C++ to provide computational efficiency and scalability for large genomic datasets.
• Companion R Package (Rsampletrees): Provides pre- and post-processing functionality including setup of input files, management of outputs, and storing and visualizing results.

Scientific Applications:

• Population Genetics: Infers historical population sizes, migration patterns, and demographic events via sampled genealogies.
• Phylogenetics: Reconstructs evolutionary relationships and histories among species or populations using genealogy samples.
• Genomic Association Studies: Provides genealogical context for interpreting associations between genetic variants and phenotypes.

Methodology:

Uses Markov chain Monte Carlo to generate samples from the posterior distribution of genealogies conditioned on phased or unphased SNP genotype data.