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HapTree specifications


Unique identifier OMICS_03445
Name HapTree
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes


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  • person_outline Emily Berger <>

Publication for HapTree

HapTree in publications

PMCID: 5954289
PMID: 29764364
DOI: 10.1186/s12864-018-4464-9

[…] various polyploid haplotype phasing methods have been developed. hapcompass [] relied on a graphical approach to develop a scheme which resolves conflicts arising from incorrect haplotype phasing. haptree [] investigated the polyploid setup using a branch-and-bound scheme. sdhap [] formulates the haplotype assembly problem as a semi-definite program and exploits its special structure, the low […]

PMCID: 5915555
PMID: 29720992
DOI: 10.3389/fpls.2018.00513

[…] overlapping sequence reads (figure )., a number of different polyploid haplotyping tools (for sequence reads) have been developed in recent years, including polyhap (), satlotyper (), hapcompass (), haptree (), sdhap (), shesisplus (), and tripoly (motazedi et al., unpublished). three of these tools (hapcompass, haptree, and sdhap) were recently compared and evaluated over a range of different […]

PMCID: 4822172
PMID: 27048905
DOI: 10.1038/srep24095

[…] the haplotypes using the shared haplotype information within the sample, given the genotypes of individuals from a population. recently, two algorithms have been proposed for haplotype assembly: haptree and hapcompass. however, not much progress has been made recently in developing the haplotype phasing algorithms for polyploids. most of these algorithms are proposed several years ago. […]

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HapTree institution(s)
Department of Mathematics, MIT, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA; Department of Mathematics, UC Berkeley, Berkeley, CA, USA
HapTree funding source(s)
NSF/NIH BIGDATA Grant R01GM108348-01; the Simons Foundation; an NSF graduate research fellowship

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