Table 1.

Notation Used to Describe the Model.

n	Number of haplotypes with the selected allele
m	Number of haplotypes without the selected allele
L	Number of SNPs flanking the selected site (one side considered at a time)
X	n × L matrix of haplotypes with the selected allele
H	m × L matrix of haplotypes without the selected allele
Xij	Allele in haplotype i at SNP j, where $i\in \{1,\mathrm{\dots },n\}$, and $j\in \{1,\mathrm{\dots },L\}$
Hzj	Allele in haplotype z at SNP j, where $z\in \{1,\mathrm{\dots },m\}$, and $j\in \{1,\mathrm{\dots },L\}$
Aj	Allele at site j on the ancestral haplotype
Zij	The reference panel haplotype from which Xi copies at site j
tca	Time to the most recent common ancestor (TMRCA)
Wi	The location of the first recombination event off of the ancestral haplotype
r	Recombination rate per basepair per generation
μ	Mutation rate per basepair per generation
θ	Haplotype miscopying rate, or population-scaled mutation rate $(4N\mu )$
ρ	Haplotype switching rate, or population-scaled recombination rate $(4Nr)$
dw	Physical distance of site w from the selected site, where $w\in \{1,\mathrm{\dots },L\}$
cj	Number of basepairs between sites j and j + 1
αiw	Likelihood of haplotype i for sites $1,\mathrm{\dots },w$
βiw	Likelihood of haplotype i for SNPs $(w+1),\mathrm{\dots },L$