Demographic Inference
Transition density functions of WF diffusion processes
and their applications
  • spectralTDF [ Link ]
    Software accompaniment to "Steinrücken, M., Jewett, E.M., and Song, Y.S. SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates, and effective population sizes. Bioinformatics, Vol. 32, No. 5 (2016) 795-797."
  • spectralHMM [ Link ]
    Software accompaniment to "Steinrücken, M., Bhaskar, A. and Song, Y.S. A novel spectral method for inferring general diploid selection from time series genetic data. Annals of Applied Statistics, Vol. 8, No. 4 (2014) 2203-2222."

  • Estimating Recombination Rates
    Accuracy of the Coalescent

    Short-Read Error Correction

    De novo Assembly

    Basecaller for the Illumina Platform

    Likelihoods under the Coalescent with Recombination

    Multi-locus Match Probability

    Whole-Genome Association Mapping

    Algorithms for Detecting Recombination