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

Matthias Steinrücken; Ethan M Jewett; Yun S Song

doi:10.1093/bioinformatics/btv627

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

Bioinformatics. 2016 Mar 1;32(5):795-7. doi: 10.1093/bioinformatics/btv627. Epub 2015 Nov 9.

Authors

Matthias Steinrücken¹, Ethan M Jewett², Yun S Song³

Affiliations

¹ Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA 01003, USA.
² Department of Statistics.
³ Department of Statistics, Department of EECS, Department of Integrative Biology, University of California, Berkeley, CA 94720, USA, Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.

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.

MeSH terms

Genetics, Population
Models, Genetic
Mutation
Mutation Rate*
Selection, Genetic

Abstract

MeSH terms

Grants and funding