Legofit: Estimating Population History from Genetic Data

Background Our current understanding of archaic admixture in humans relies on statistical methods with large biases, whose magnitudes depend on the sizes and separation times of ancestral populations. To avoid these biases, it is necessary to estimate these parameters simultaneously with those describing admixture. Genetic estimates of population histories also confront problems of statistical identifiability: different models or different combinations of parameter values may fit the data equally well. To deal with this problem, we need methods of model selection and model averaging, which are lacking from most existing software. Results The Legofit software package allows simultaneous estimation of parameters describing admixture and other aspects of population history. It includes facilities for data manipulation, estimation, model selection, and model averaging. It outperforms several statistical methods that have been widely used to study archaic admixture in humans.