Mongrail2 version 2.1

The latest release of Mongrail2 (v2.1.0) is available at mongrail2/releases/tag/v2.1.0. Mongrail2 is a program for Bayesian inference of hybrid genealogy from population genetic data. It classifies individuals as purebred or hybrid based on multilocus genotype data from two reference populations, computing log-likelihoods and posterior probabilities for six genealogical models representing different hybrid categories.

Changes in v2.1

  • Added support for phased data with direct O(H) likelihood computation for fully phased hybrid data and automatic detection of phased vs unphased input.
  • Implemented sparse enumeration for recombination configurations using an O(n^k) algorithm instead of O(2^n), with a new -k option to set the maximum number of recombinations (default: 4).
  • Optimized Q computation by exploiting the symmetry Q(z) = Q(~z), reducing computation by approximately 50%.

Pre-built binaries are available for Linux (x86_64), macOS (Apple Silicon), and Windows (x86_64) on the releases page.