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Protocols

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

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for HaploBlockFinder

HaploBlockFinder citations

 (9)
library_books

Naturally Occurring Genetic Variants in Human DC SIGN Increase HIV 1 Capture, Cell Transfer and Risk of Mother To Child Transmission

2012
PLoS One
PMCID: 3393705
PMID: 22808239
DOI: 10.1371/journal.pone.0040706

[…] 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 were s […]

library_books

Functional Genetic Variants in DC SIGNR Are Associated with Mother to Child Transmission of HIV 1

2009
PLoS One
PMCID: 2752805
PMID: 19809496
DOI: 10.1371/journal.pone.0007211

[…] f 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 genotype […]

call_split

Molecular Population Genetics of Human CYP3A Locus: Signatures of Positive Selection and Implications for Evolutionary Environmental Medicine

2009
Environ Health Perspect
PMCID: 2790508
PMID: 20019904
DOI: 10.1289/ehp.0800528
call_split See protocol

[…] e correction for multiple testing. We used GOLD software () as described by ) to draw the LD maps.Haplotypes were constructed using the Phase 2.0 program (). We then partitioned haplotype blocks with HaploBlockFinder () as described by . The mutational relationships among haplotypes in CYP3A43 and CYP3A5 were shown by constructing minimum-spanning trees (MSTs), with the common chimpanzee as an out […]

library_books

Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies

2008
BMC Genomics
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, they we […]

library_books

Canine Population Structure: Assessment and Impact of Intra Breed Stratification on SNP Based Association Studies

2007
PLoS One
PMCID: 2129117
PMID: 18091995
DOI: 10.1371/journal.pone.0001324

[…] .1 with the default settings. This software estimates the missing genotypes and reconstructs haplotypes using unphased genotype data from unrelated individuals. Haplotype blocks were determined with HaploBlockFinder program, v0.7, using SNP with MAF>0.05 . Association studies simulations were conducted with Haploview_4.0beta14 and PLINK_0.99q packages. […]

library_books

Incorporating Single Locus Tests into Haplotype Cladistic Analysis in Case Control Studies

2007
PLoS Genet
PMCID: 1829402
PMID: 17381242
DOI: 10.1371/journal.pgen.0030046

[…] r 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, and […]


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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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