SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes.

Abstract

MOTIVATION: In the Wright-Fisher diffusion, the transition density function describes the time evolution of the population-wide frequency of an allele. This function has several practical applications in population genetics and computing it for biologically realistic scenarios with selection and demography is an important problem. RESULTS: We develop an efficient method for finding a spectral representation of the transition density function for a general model where the effective population size, selection coefficients and mutation parameters vary over time in a piecewise constant manner. AVAILABILITY AND IMPLEMENTATION: The method, called SpectralTDF, is available at https://sourceforge.net/projects/spectraltdf/ CONTACT: yss@berkeley.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.