Supplemental material

for

Incorporating Genotyping Uncertainty in Haplotype Inference for Single-Nucleotide Polymorphisms

Hosung Kang, Zhaohui S. Qin, Tianhua Niu and Jun S. Liu

· Three programs are developed for haplotype inference with genotyping uncertainty:

(1) GeneScore : Tmixture program (input: FI values)

(2) GeneSpec : generates genotype spectrum using output files from GeneScore (1).

(3) EM-II : Phasing program using the output from GeneSpec (2).

· To receive update notice and bug fixes of these programs, please register with us here. Thank you.

· This research was partly supported by the NSF Grants DMS-0094613, DMS-0104129 and NIH Grant HG002518-01 to JSL