PT - JOURNAL ARTICLE AU - Matthias Steinrücken AU - Ethan M. Jewett AU - Yun S. Song TI - SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates, and effective population sizes AID - 10.1101/029736 DP - 2015 Jan 01 TA - bioRxiv PG - 029736 4099 - http://biorxiv.org/content/early/2015/10/23/029736.short 4100 - http://biorxiv.org/content/early/2015/10/23/029736.full AB - In the Wright-Fisher diffusion, the transition density function (TDF) 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. We develop an efficient method for finding a spectral representation of the TDF for a general model where the effective population size, selection coefficients, and mutation parameters vary over time in a piecewise constant manner. The method, called spectralTDF, is available at https://sourceforge.net/projects/spectraltdf/.