Skip to main content Skip to navigation

haplotype analysis

    Data from here: http://linkage.rockefeller.edu/soft/list1.html

    • BEAGLE
    • full name:
    • version: 3.2.1 (May 2010)
    • descriptions: BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can
      * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios.
      * infer sporadic missing genotype data.
      * impute ungenotyped markers that have been genotyped in a reference panel.
      * perform single marker and haplotypic association analysis.
      * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals.
    • authors: Brian L Browning, Sharon R Browning (email: browning@stat.auckland.ac.nz),
    • web/ftp:http://www.stat.auckland.ac.nz/~browning/beagle/beagle.html
    • source code language: Java
    • operating systems: MS-Windows, Linux, UNIX(Solaris), MacOS
    • executables:
    • reference: Browning SR and Browning BR (2007), "Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering", American Journal of Human Genetics, 81(5):1084-1097. [html]
      Browning BR and Browning SR (2007), "Efficient multilocus association testing for whole genome association studies using localized haplotype clustering", Genetic Epidemiology, 31:365-375.


    • BEAGLECALL 
      • full name:
      • version: 1.0.0 (September 2010)
      • descriptions: BEAGLECALL is a software package for simultaneous genotype calling and haplotype phasing for unrelated individuals. BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes. BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes. BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation.
      • authors:
      • web/ftp: http://faculty.washington.edu/browning/beaglecall/beaglecall.html
      • source code language: Java
      • operating systems: MS-Windows, UNIX, Linux, MacOS
      • executables:
      • reference: Browning, Yu (2009), "Simultaneous genotype calling and haplotype phase inference improves genotype accuracy and reduces false positive associations for genome-wide association studies", American Journal of Human Genetics, 85:847-861.


      • full name: Berkeley method for Perfect Phylogeney Haplotyping
      • version: April 2003
      • descriptions: a program for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent). In population genetic terms, BPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model.
      • authors: Ren-Hua Chuang, Dan Gusfield (UC Davis) (email: gusfield@cs.ucdavis.edu)
      • web/ftp:http://wwwcsif.cs.ucdavis.edu/~gusfield/bpph.html
      • source code language:
      • operating systems:
      • executables:
      • reference: D. Gusfield (2002), "Haplotyping as perfect phylogeny: conceptual framework and efficient solutions", In Proceedings of RECOMB, Sixth Annual Conference on Research in Computational Molecular Biology, pp.?-?.



          • ENTROPY BLOCKER
            • full name:
            • version: 1.7
            • descriptions: aiming at identifying "haplotype blocks". The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low.
            • authors:
            • web/ftp: http://wpicr.wpic.pitt.edu/WPICCompGen/blocks.htm
            • source code language: R
            • operating systems: MS-Windows, Linux
            • executables:
            • reference:




                • GENIE
                  • full name:
                  • version: 2.7.2.1 (2010)
                  • descriptions: GENIE (previously PEDGENIE and HAPMC) performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests.
                  • authors: Nicola Camp, K Allen-Brady, Jathine Wong, K Curtin, R Abo
                  • web/ftp: http://bioinformatics.med.utah.edu/Genie/index.html
                  • source code language: Java 1.6
                  • operating systems: web-based
                  • executables: PedGenie, hapMC, hapConstructor
                  • reference: Allen-Brady, Farnham, Weiler, Camp (2003), "A cautionary note on the appropriateness of using a linkage resource for an association study", BMC Genetics, 4(suppl 1):S89.
                    Allen-Brady, Wong, Camp (2006), "PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size", BMC Bioinformatics, 7:209.
                    Curtin, Wong, Allen-Brady, Camp (2007), "PedGenie: meta genetic association testing in mixed family and case-control designs", BMC Bioinformatics, 8:448.
                    Abo, Knight, Wong, Cox, Camp (2008), "hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework", Bioinformatics, 24(18):2105-2107.



                    • HAPBLOCK
                      • full name:a dynamical programming algorithm for haplotype block partitioning
                      • version: 2002
                      • descriptions:
                      • authors:Kui Zhang, Fengzhu Sun (USC)
                      • web/ftp: http://www-hto.usc.edu/msms/HapBlock/
                      • source code language:C
                      • operating systems:MS-Windows, Linux, UNIX(Solaris)
                      • executables:
                      • reference: Kui Zhang, Minghua Deng, Ting Chen, Michael S Waterman, Fengzhu Sun (2002),Proceddings of the National Academy of Sciences , 99:7335-7339.
                        Zhang, Qin, Chen, Liu, Waterman, Sun (2005), "HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms",Bioinformatics, 21(1):131-134.



                        • HAPLOBLOCKFINDER
                          • full name:
                          • version: 0.7
                          • descriptions: HaploBlockFinder is a package for haplotype block identification, visualization and htSNP selection. It can also compare the haplotype block structure with local LD pattern. The program can be either run as a web service, or standalone executables on local machine.
                          • authors: Kun Zhang (kun.zhang@uth.tmc.edu)
                          • web/ftp: http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi
                          • source code language: C and Perl
                          • operating systems: UNIX, MS-Windows
                          • executables: haploBlockFinder, hbfWrapper.pl, showLDmatrix.pl, drawBlocks.pl
                          • reference:


                          • HAPLOBUILD
                            • full name:
                            • version:
                            • descriptions: The analysis of large amounts of SNP data creates difficulties for the analysis of haplotypes and their association to traits of interest. Commonly fairly simple methods, such as two- or three-SNP sliding windows are used to create haplotypes across large regions, but these may be of limited value when adjacent SNPs are in strong LD and provide redundant information. We have created a novel program, "HaploBuild" for constructing and testing haplotypes for SNPs in close physical proximity to one another but which are not necessarily contiguous. Furthermore, the number of SNPs contained in the haplotype is not restricted, thereby permitting the evaluation of complex haplotype structures.
                            • authors: JM Laramie, JB Wilk, AL DeStefano, RH Myers (Boston University)
                            • web/ftp: http://snp.bumc.bu.edu/modules.php?name=HaploBuild
                            • source code language: Perl
                            • operating systems: Linux, MS-Windows, MacOS
                            • executables:
                            • reference: Laramie, Wilk, DeStefano, Myers (2007), "HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies", Bioinformatics, 23(16):2190-2192.



                              • HAPLOVIEW
                                • full name:
                                • version: 3.32 (May 2006)
                                • descriptions: Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable.
                                • authors: Jeffrey Barrett (Whitehead Institute)
                                • web/ftp: http://www.broad.mit.edu/personal/jcbarret/haploview/
                                • source code language: Java
                                • operating systems:
                                • executables:
                                • reference: Barrett, Fry, Maller, Daly (2005), "Haploview: analysis and visualization of LD and haplotype maps", Bioinformatics, 21(2):263-265.




                                  • HIT 
                                    • full name: Haplotype Inference Technique
                                    • version:
                                    • descriptions:
                                    • authors: Pasi Rastas
                                    • web/ftp: http://www.cs.helsinki.fi/u/prastas/hit/
                                    • source code language: java
                                    • operating systems:
                                    • executables:
                                    • reference: Rastas, Koivisto, Mannila, Ukkonen (2005), "A Hidden Markov Technique for Haplotype Reconstruction", 5th Workshop on Algorithms in Bioinformatics - WABI 2005
                                      Rastas, Koivisto, Mannila, Ukkonen (2008), "Phasing genotypes using a hidden Markov model", in eds. I Mandoiu and A Zelikovsky, Bioinformatics Algorithms: Techniques and Applications, pp. 373-391 (Wiley).



                                    • LDGROUP
                                      • full name:
                                      • version: Nov 2007
                                      • descriptions: inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs.
                                      • authors: Fumihiko Takeuchi (email: fumihiko@takeuchi.name)
                                      • web/ftp: http://www.fumihiko.takeuchi.name/publications.html
                                      • source code language: R
                                      • operating systems:
                                      • executables:
                                      • reference: Takeuchi, Yanai, Morii, Ishinaga, Taniguchi-Yanai, Nagano, Kato (2005), "Linkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs", Genetics, 170:291-304.




                                      • PHASE
                                        • full name:
                                        • version: 2.0 (Sept 2003)
                                        • descriptions: This program implements a new statistical method for reconstructing haplotypes from population genotype data
                                          new for v2: (1) the introduction of a new computational approach, resulting in much faster haplotype resolution. (2) the introduction of a new model that allows for recombination and decay of Linkage Disequilibrium (LD) with distance, which results in more accurate haplotype estimates. This model also allows the user to estimate recombination rates, and identify recombination hotspots from population genotype data. (3) the facility to perform a test for haplotype frequency differences between cases and controls. (4) more extensive output summarising the results.
                                        • Authors: Matthew Stephens (email: stephens@stat.washington.edu)
                                        • web/ftp: http://www.stat.washington.edu/stephens/software.html 
                                          previous site: http://www.stats.ox.ac.uk/mathgen/software.html
                                        • source code language:
                                        • operating systems:
                                        • executables:
                                        • reference: Stephens, Smith, Donnelly (2001), AJHG, 68:978-989.


                                        • PL-EM
                                          • full name: Partition-Ligation EM algorithm for haplotype inference with single nucleotide polymorphisms
                                          • version:
                                          • descriptions:
                                          • authors: Jun Liu, Steve Qin, Tianhua Niu (Harvard Univ)
                                          • web/ftp: http://www.people.fas.harvard.edu/~junliu/plem/
                                          • source code language:
                                          • operating systems:
                                          • executables:
                                          • reference: Qin, Niu, Liu (2002), "Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms", American Journal of Human Genetics, (letter), 71(5):1242-1247-?. [html]



                                          SWEEP 

                                            • full name:
                                            • version: December 2005
                                            • descriptions: SWEEP allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection. Primarily, it uses the Long Range Haplotype test to look for alleles of high frequency with long-range linkage disequilibrium, which suggest the haplotype rapidly rose to high frequency before recombination could break down associations with nearby markers. SWEEP takes phased genotype data as input, detects all haplotype blocks in that data, and then determines the frequency and long-range LD for each allele in each block.
                                            • authors: Patrick Varilly, Ben Fry, Oleg Shamovsky, Pardis Sabeti (email: sweep@broad.mit.edu)
                                            • web/ftp: http://www.broad.mit.edu/mpg/sweep/
                                            • source code language:
                                            • operating systems:
                                            • executables:
                                            • reference: Sabeti, Reich, Higgins, Levine, Richter, Schaffner, Gabriel, Platko, Patterson, McDonald, Ackerman, Campbell, Altshuler, Cooper, Kwiatkowski, Ward, Lander (2002), "Detecting recent positive selection in the human genome from haplotype structure", Nature, 419:832-827.




                                                • TREESCAN

                                                  • full name:
                                                  • version: 0.9
                                                  • descriptions: TREESCAN is intended to provide p-values for the hypothesis of association between evolutionary clades and continuous traits, using haplotype trees.
                                                  • authors: David Posada (email: dposada@uvigo.es)
                                                  • web/ftp: http://darwin.uvigo.es/software/treescan.html
                                                  • source code language: C
                                                  • operating systems: UNIX, MS-Windows, MS-DOS, MacOS(X)
                                                  • executables:
                                                  • reference: Posada, Maxwell, Templeton (2005), "TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees", Bioinformatics, 21(9):2130-2132.