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Halperin, E., & Eskin E. (2004).  Haplotype Reconstruction from Genotype Data Using Imperfect Phylogeny. Bioinformatics.
Halperin, E., & Hazan E. (2005).  Haplofreq - Estimating Haplotype Frequencies Efficiently. Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB'05). 553-568.