When you use HAP, please cite:

• Eran Halperin, Eleazar Eskin. ``Haplotype Reconstruction from Genotype Data using Imperfect Phylogeny.'' Bioinformatics. 20(12):1842-9.

Other papers related to HAP:

• Eleazar Eskin, Eran Halperin, Richard Karp. ``Efficient Reconstruction of Haplotype Structure via Perfect Phylogeny.'' Journal of Bioinformatics and Computational Biology. 1(1):1-20.



• Eleazar Eskin, Eran Halperin, Richard Karp. ``Large Scale Reconstruction of Haplotypes from Genotype Data.'' In Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB-2003). 104-113.



• Eleazar Eskin, Eran Halperin, Roded Sharan. "Optimally Phasing Long Genomic Regions using Local Haplotype Predictions". Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, 2004.



• Eran Halperin and Richard M. Karp. "Perfect Phylogeny and Haplotype Assignment". In Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB-2004)



• Eran Halperin and Elad Hazan "HAPLOFREQ - Estimating Haplotype Frequencies Efficiently". To appear in Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB-2005)

Papers that use HAP for disease association studies or others

• Bertram L, Menon R, Mullin K, Parkinson M, Bradley ML, Blacker D, Tanzi RE. "PEN2 is not a genetic risk factor for Alzheimer's disease in a large family sample." Neurology. 2004 Jan 27;62(2):304-6.