• Haploview

  • Referenced in 22 articles [sw11870]
  • Haploview: analysis and visualization of LD and haplotype maps. Research over the last few years ... revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly ... computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data...
  • HAPLO

  • Referenced in 23 articles [sw04580]
  • Estimate the Frequencies of Multi-site Haplotypes...
  • RPOLY

  • Referenced in 10 articles [sw05301]
  • Haplotype inference with pseudo-Boolean optimization. The fast development of sequencing techniques in the recent ... urgent development of efficient and accurate haplotype inference tools. Besides being a crucial issue ... genetics, haplotype inference is also a challenging computational problem. Among others, pure parsimony ... modeling approach to solve the problem of haplotype inference and also an interesting NP-hard...
  • MaCH

  • Referenced in 7 articles [sw17274]
  • Using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genome-wide association studies ... evaluated indirectly using either genotyped markers or haplotypes thereof as proxies. We have previously implemented ... Markov Chain framework for genotype imputation and haplotyping in the freely available MaCH software package ... sequence data to estimate unobserved genotypes and haplotypes, together with useful measures of the quality...
  • HapCUT

  • Referenced in 6 articles [sw35352]
  • efficient and accurate algorithm for the haplotype assembly problem. Motivation: The goal of the haplotype ... assembly problem is to reconstruct the two haplotypes (chromosomes) for an individual using ... problem. In this article, we consider the haplotype assembly problem in the most general setting ... describe a novel combinatorial approach for the haplotype assembly problem based on computing max-cuts...
  • HapBlock

  • Referenced in 5 articles [sw26434]
  • HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming ... SNPs. Compared to other programs for haplotype block partitioning and tag SNP selection, our program ... blocks and tag SNPs. Second, both haplotype data and genotype data from unrelated individuals and/or ... analyzed. Third, several existing measures/criteria for haplotype block partitioning and tag SNP selection have been...
  • UNPHASED

  • Referenced in 6 articles [sw20040]
  • treatment of missing genotype data and uncertain haplotypes; Global association tests and tests of individual ... haplotypes; Conditioning tests that allow for previous associations of linked loci; Inclusion of information from...
  • WhatsHap

  • Referenced in 4 articles [sw23105]
  • WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. The human genome is diploid, which ... copies of the genome. The resulting haplotypes, lists of SNPs belonging to each copy ... information, constitute the state-of-the-art. Haplotype assembly, which addresses phasing directly from sequencing ... from higher sequencing error rates. Currently, no haplotype assembly approaches exist that allow for taking...
  • LAMP

  • Referenced in 5 articles [sw33854]
  • admixed individuals as well as reference haplotype panels pproximating the mixing ancestral populations, and outputs ... includes the program LAMP-HAP, which processes haplotype data when high-quality phasing is available...
  • GERBIL

  • Referenced in 4 articles [sw17194]
  • accurate resolution (phasing) of the genotypes into haplotypes. We present here results on a method ... recombination-poor regions (”blocks”), in which haplotypes are generated from a small number of core ... haplotypes, allowing for mutations, rare recombinations, and errors. We formulate genotype resolution and block partitioning...
  • HapSim

  • Referenced in 4 articles [sw35553]
  • HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies ... simulation tool HapSim for the generation of haplotype data. The simulated haplotypes are such that...
  • SimPed

  • Referenced in 3 articles [sw15080]
  • SimPed: A simulation program to generate haplotype and genotype data for pedigree structures. With ... there is great interest in analyzing pedigree haplotype data. Intermarker linkage disequilibrium for microsatellite markers ... programs available which can generate haplotype and/or genotype data consisting of a large number ... SimPed is a program that quickly generates haplotype and/or genotype data for pedigrees of virtually...
  • ReFHap

  • Referenced in 3 articles [sw35232]
  • reliable and fast algorithm for single individual haplotyping. Full human genomic sequences have been published ... mixed consensus of the two real haplotypes because it is still very expensive to separate ... through bioinformatics methods such as single individual haplotyping. Full haploid sequences provide a complete understanding ... novel problem formulation for single individual haplotyping. We start by assigning a score to each...
  • HAPGEN2

  • Referenced in 6 articles [sw17354]
  • association studies. Simulation based on resampling known haplotypes is fast and efficient and can produce...
  • CompactCH

  • Referenced in 4 articles [sw34255]
  • population divergence history) from population haplotypes. Simulation results show that the CompactCH algorithm enables efficient ... inference of population trees with much more haplotypes than a previous approach. Availability: The CompactCH...
  • haplo.stats

  • Referenced in 3 articles [sw20042]
  • package haplo.stats: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous ... Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects ... unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers...
  • hapassoc

  • Referenced in 3 articles [sw25734]
  • hapassoc: Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm ... used for inference of trait associations with haplotypes and other covariates in generalized linear models ... cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some...
  • Tree-k-RHC

  • Referenced in 2 articles [sw20976]
  • efficient algorithm for haplotype inference on pedigrees with a small number of recombinants. Combinatorial ... rule-based) methods for inferring haplotypes from genotypes on a pedigree have been studied extensively ... These methods generally try to reconstruct the haplotypes of each individual so that the total ... question of how to efficiently infer haplotypes on a large pedigree when the number...
  • 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...