HaploBlockFinder statistics

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HaploBlockFinder specifications

Information


Unique identifier OMICS_13929
Name HaploBlockFinder
Interface Web user interface
Restrictions to use None
Input format FASTA, MERLIN, ARLEQUIN, PHASE
License GNU General Public License version 3.0
Computer skills Basic
Version 0.7
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_13929
Name HaploBlockFinder
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format FASTA, MERLIN, ARLEQUIN, PHASE
Operating system Unix/Linux, Windows
Programming languages C, Perl
License GNU General Public License version 3.0
Computer skills Medium
Version 0.7
Stability No
Maintained No

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Publication for HaploBlockFinder

HaploBlockFinder in publications

 (7)
PMCID: 3393705
PMID: 22808239
DOI: 10.1371/journal.pone.0040706

[…] iu (22,9%), ip (48%) and pp periods (29.1%) ., haplotype reconstruction was performed as previously described . haplotype-tagged single nucleotide polymorphisms (htsnps) were determined using the haploblockfinder software with a minor allele frequency over 5% and numbers were redefined compared to our previous publication for their frequency in the present study population. ten htsnps […]

PMCID: 2752805
PMID: 19809496
DOI: 10.1371/journal.pone.0007211

[…] 2%. we applied the algorithm five times, using different randomly generated seeds, and consistent results were obtained across runs (). fifteen haplotype-tagged snps (htsnps) were identified by the haploblockfinder software with a maf ≥5%. these htsnps were genotyped in the 197 infants by direct pcr sequencing analysis as we have described previously . the dc-signr exon 4 repeat region […]

PMCID: 2547855
PMID: 18759977
DOI: 10.1186/1471-2164-9-405

[…] of ld-based approaches and those given by limited haplotype diversity methods. additionally, future work could consider the comparison between blocking and using tagging snps. two useful approaches, haploblockfinder [] and htsnper [], produce both haplotype or ld blocks, and tagging snps. as they yield block partitions similar to those of methods already covered by haploview and hapblock, […]

PMCID: 1829402
PMID: 17381242
DOI: 10.1371/journal.pgen.0030046

[…] method can be used in wga studies by the following procedures: (1) haplotype reconstruction (softwares are available, such as haplotyper [] or phase []) and haplotype block partition (htsnper [] or haploblockfinder []) for whole genome genotype data; (2) in each haplotype block, reconstruct the hierarchical tree within each of the sliding windows using the weighted haplotype distance metric, […]

PMCID: 1698582
PMID: 17137522
DOI: 10.1186/1471-2105-7-525

[…] that performs ld and haplotype block analysis on publicly available or user supplied genotype data. htsnper1.0 [] and haploblock [] can also be used to analyze genotype data supplied by users. haploblockfinder [] is a web-based tool that allows for the inference of haplotype blocks and tag snp selection from genotype data uploaded by users. the genome variation server (gvs) [] […]


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HaploBlockFinder institution(s)
Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
HaploBlockFinder funding source(s)
Supported by the Rosalie B. Hite Foundation.

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