HapTree is a tool for haplotype reconstruction from sequencing data (e.g. Illumina) of a single individual genome that maybe diploid or have higher ploidy. This tool implements a maximum-likelihood estimation framework to assemble haplotypes. HapTree has a high switch accuracy within phased haplotype blocks.
Berger E, Yorukoglu D, Peng J, Berger B "HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data." PLoS Comput Biol. 2014 Mar 27;10(3):e1003502. eCollection 2014 Mar. https://doi.org/10.1371/journal.pcbi.1003502
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