HaploRec: Efficient and
accurate large-scale reconstruction of haplotypes
HaploRec [1,2] is a statistical haplotype reconstruction algorithm
targeted for large-scale disease association studies. It is especially
suitable for data sets with a large number of subjects and
a large number of possibly sparsely located markers.
HaploRec is implemented in the Java programming language, and thus works on any platform
for which a java virtual machine is available (practically all common operating systems). It requires Java virtual machine 1.5 or higher.
References
Obtaining HaploRec
HaploRec is freely available for academic, non-commercial use. Commercial use requires a license.
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Click here to
obtain an academic license and download HaploRec (version 2.3).
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Click here for information on commercial licensing.
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Download HaploRec documentation
Version history
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2.3 (February 2008) Current version. Introduces an improved Markov model,
where the conditional probabilities are smoothed over several different
context lengths. This is now the default model. More efficient splitting
and combining of files in the windowing version intended for chromosome-wide data sets. Minor improvements in memory management.
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2.2 (May 2007) Conceptually identical to version 2.1.
Extension program which enables handling of chromosome-wide data sets is now
implemented in java instead of perl, improving platform independence.
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2.1 (September 2006) The version described in [1]. Introduces an improved
segmentation model that gives more accurate results
than the segmentation model used in version 2.0.
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2.0 (June 2005) This version introduced an EM-based algorithm and
a segmentation-based haplotype probability model, and
featured several computational improvements, allowing
the use of larger data sets.
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1.0 (January 2004) Original implementation of the algorithm introduced in [2].
Used a variable-order markov model. Used a simple
"optimistic matching" strategy for fragment frequency estimation
(instead of the EM algorithm used by the later versions).
Data sets