METHODOLOGY ARTICLE

Coalescent simulation is a very useful tool in population genetics with a rich variety of applications, particularly to evaluate and compare performances of various statis-tical methods in rare variant analysis [1-3], to estimate parameters for different population histories [4,5] and to infer phylogenetic trees [6]. In simulating DNA sequence data for studying human complex diseases, recombin-ation hotspots, defined as genomic intervals with local recombination rates increased relative to that of the sur-rounding DNA region, need to be taken into account given their ubiquity in the human genome [7]. Further, population geneticists are interested in examining haplo-type block patterns delineated by recombination hot-spots along chromosomes in fine-mapping locations of disease loci. Over the past decade, a plethora of coales- * Correspondence