Legofit

Legofit estimates population history parameters from nucleotide site pattern frequencies to infer admixture, ancestral population sizes, and separation times.

Key Features:

• Simultaneous Parameter Estimation: Estimates admixture events together with ancestral population sizes and separation times to reduce biases from separate estimation.
• Model Selection and Averaging: Implements model selection and averaging methods to address statistical identifiability among competing demographic models and parameter combinations.
• Data Manipulation and Analysis: Provides facilities for data manipulation, parameter estimation processes, and residual analysis of fit to nucleotide site pattern data.
• Focus on Deep Population History: Emphasizes inference of deep historical population size, subdivision, and admixture rather than recent population history.

Scientific Applications:

• Evolutionary history reconstruction: Reconstructs ancestral relationships among populations using DNA sequence data from multiple populations.
• Admixture and migration inference: Infers archaic admixture events and historical migration patterns from nucleotide site pattern frequencies.
• Cross-species demographic studies: Applies to genetic datasets from various species to study deep demographic events beyond human populations.

Methodology:

Uses counts of nucleotide site patterns as the basis for estimating historical population parameters.