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

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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.

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