SNPHAP, PL-EM, and HaploRec were roughly based on the HWE and EM algorithm, while fastPHASE was based on the coalescence model and the MCMC method (Stephens and Donnelly 2003; Marchini et al. 2006).

Xiao-Li Meng, David van Dyk, The EM Algorithm--An Old Folk-Song Sung to a Fast New Tune, Journal of the Royal Statistical Society. Series B (Methodological), Vol. 59, No. 3 (1997), pp. 511-567. Link ...

Ying Zhang, Mortaza Jamshidian, On Algorithms for the Nonparametric Maximum Likelihood Estimator of the Failure Function with Censored Data, Journal of Computational and Graphical Statistics, Vol. 13, ...