• htSNPer1.0

  • Referenced in 2 articles [sw35554]
  • htSNPer1.0: software for haplotype block partition and htSNPs selection. Results: A heuristic algorithm, generalized branch ... searching of minimal set of haplotype tagging SNPs (htSNPs) according to different htSNPs performance criteria ... integrate three htSNPs performance criteria and four haplotype block definitions for haplotype block partitioning ... which can be used to characterize the haplotype block structure and select htSNPs...
  • HaploBlockFinder

  • Referenced in 2 articles [sw30041]
  • HaploBlockFinder: haplotype block analyses. Summary: Recent studies have unveiled discrete block-like structures of linkage ... analyze the block-like LD structures (haplotype blocks) based on haplotype data. Three definitions ... haplotype block are supported, including minimal LD range, no historic recombination, and chromosome coverage. Tagged ... SNPs that uniquely distinguish common haplotypes are identified. A greedy algorithm was used to improve...
  • CollHaps

  • Referenced in 2 articles [sw35234]
  • CollHaps: A Heuristic Approach to Haplotype Inference by Parsimony. Haplotype data play a relevant role ... populations. However, the experimental determination of haplotypes is expensive and time-consuming. This motivates ... increasing interest in techniques for inferring haplotype data from genotypes, which can instead be obtained ... theoretical arguments. However, the problem of haplotype inference by parsimony was shown...
  • HAPLORE

  • Referenced in 2 articles [sw36930]
  • HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Results: We test ... families have one unique haplotype configuration. In the presence of missing data, the number ... compatible haplotypes can be substantially reduced by HAPLORE, and the program will provide all possible ... haplotype configurations of a pedigree under different circumstances, if such multiple configurations exist. These inferred...
  • TreeDT

  • Referenced in 2 articles [sw37015]
  • method. Given a set of disease-associated haplotypes and a set of control haplotypes, TreeDT ... TreeDT extracts, essentially in the form of haplotype trees, information about historical recombinations ... population: A haplotype tree constructed at a given chromosomal location is an estimate ... genealogy of the haplotypes. TreeDT constructs these trees for all locations on the given haplotypes...
  • SNPStats

  • Referenced in 3 articles [sw20043]
  • gene-environment). Analysis of multiple SNPs: haplotype frequency estimation, analysis of association of haplotypes with...
  • HaploRec

  • Referenced in 2 articles [sw35409]
  • efficient and accurate large-scale reconstruction of haplotypes. Results: We define three novel statistical models ... give an efficient algorithm for haplotype reconstruction, jointly called HaploRec. HaploRec is based on exploiting ... local regularities conserved in haplotypes: it reconstructs haplotypes so that they have maximal local coherence ... powerful method for the large scale haplotyping needed in association studies. With sample sizes large...
  • SNPassoc

  • Referenced in 4 articles [sw07122]
  • binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related...
  • pegas

  • Referenced in 4 articles [sw08307]
  • writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population...
  • disclapmix

  • Referenced in 4 articles [sw14230]
  • modelling the distribution of Y chromosomal haplotypes as described in [1, 2] (refer...
  • GENEHUNTER

  • Referenced in 4 articles [sw18773]
  • addition to computation of linkage statistics and haplotype determination, GENEHUNTER can also perform single-locus...
  • genetics

  • Referenced in 4 articles [sw24196]
  • data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers...
  • SABER

  • Referenced in 4 articles [sw33848]
  • ancestral LD; however it does not model haplotype structure. Input files are typical and include...
  • PedGenie

  • Referenced in 4 articles [sw35514]
  • time, composite genotype tests, and haplotype analyses may all be performed. We illustrate the validity...
  • SpeedHap

  • Referenced in 2 articles [sw35353]
  • accurate heuristic for the single individual SNP haplotyping problem with many gaps, high reading error ... present in a chromosome (called the haplotype) is of interest in a wide area ... heuristic method for the problem of haplotype reconstruction for (portions of) a pair of homologous...
  • mirf

  • Referenced in 2 articles [sw26718]
  • This package applies a combination of missing haplotype imputation via the EM algorithm of Excoffier ... Slatkin(1995) and modelling trait-haplotype associations via the Random Forest algorithm. The EM algorithm...
  • snp.plotter

  • Referenced in 2 articles [sw30540]
  • values using single SNP and/or haplotype data. Main features of the package include options ... created using global and/or individual haplotype p-values along with single SNP p-values. Images...
  • FastMap

  • Referenced in 3 articles [sw20452]
  • perform both single marker mapping and haplotype association mapping over an m-SNP window. These...
  • FTEC

  • Referenced in 3 articles [sw24692]
  • coalescent simulation program capable of simulating haplotype samples drawn from a population that has undergone...
  • gap

  • Referenced in 3 articles [sw24918]
  • association analysis involving genetic markers including haplotype analysis with or without environmental covariates...