Haplotype
- Haplore 2.42 – Haplotype Reconstruction in pedigrees
- hapsembler 2.11 – Haplotype-specific Genome Assembly Toolkit
- Haploscribe 0.1.0 – Chromosomal Haplotypes by Genetic Phasing of Human Families
- LDMhap – LD Mapping with Haplotype Data
- SimPed – Generate Haplotype and Genotype data for Pedigree Structures
- HapSeq 2 – Haplotype Phasing and Genotype Calling from Next Generation Sequencing Data Using Haplotype Information of Jumping Reads
- mtDNASeqback 20050407 – Recover mtDNA Sequence data from Haplotype data
- hapassoc 1.2-6 – Inference of Trait Associations with SNP Haplotypes and other attributes using the EM Algorithm
- HAPI-UR 1.01 – HAPlotype Inference for UnRelated samples
- GLASCOW – Haplotype-based Association Mapping for Binary Traits in Structured Populations
- ChromoPainter 0.0.2 – Find Haplotypes in Sequence Data
- HapMiner 1.1 – Haplotype-based Linkage Disequilibrium mapping via direct Data Mining
- ShoRAH 0.6 – Short Reads Assembly into Haplotypes
- HapTagger – Tag SNP Selection Using Haplotype
- HMC 0.9.1 – Haplotype Inference tool based on Markov Chain model
- Hapler 1.60 – Haplotype Phasing of Population-sourced Sequence data
- SNaP – Simulation of sNp haplotype data And Phenotypic traits
- HAPPY 1.2 – Reconstruct HAPlotYpes
- Tomcat 1.0 – Haplotype Sharing Analysis using Mantel Statistics
- 2SNP 1.7 – Scalable Phasing based on 2-SNP Haplotypes
- neighborjoin / genostat/ haplostat – Explore Disease Susceptibility Prediction on Genotype/Haplotype data
- HapForest – Forest for Detecting Haplotypes and Interactions
- FAMHAP 19 beta – Haplotype Association Analysis Software
- HTR – Haplotype Trend Regression
- HAPLOT 3.2 – Graphical Presentation of Haplotype Block Structures
- HaploRec 2.3 – Haplotype Population-based Genotype data
- HapBlock 3.0 – Haplotype Block Partitioning
- DASH 1.1.0 – DASH Associates Shared Haplotypes
- Entropy – Uses an EM algorithm for Haplotype Frequency Estimation
- SNPHAP 1.3.1 – Estimate Frequencies of Haplotypes of SNPs
- Ligate Haplotypes 0.04 – Ligate Haplotypes with Two Overlapping Regions
- Concatenate Haplotypes 0.03 – Concatenate Two Sets of Haplotypes
- HXE 1.0 – Haplotype Environment Interaction Analysis software
- Chaplin 1.2.3 – Case-control Haplotype Inference package
- eHAP 2.0 – Analyze Multilocus data as Haplotypes
- Haplo Stats 1.5.2 – Statistical Methods for Haplotypes When Linkage Phase is Ambiguous
- HAPMIXMAP 1.0 – Model HapMap Haplotypes
- Haploclusters – Detect Excess Haplotypes Sharing
- Hapstep 20010312 – Stepwise Analysis of Diversity for Haploid Data with Distance between Haplotypes
- XQTL 1.0 – Gamily-based Allelic/Haplotype Association Test
- TreeScan 1.0 – Genotype-phenotype Associations from Haplotype Trees
- SNPYGoat 1.0 – Identify Several Goat Y-chromosomal Haplotypes
- HapYDive – Excel Plugin for Y-STR Haplotype Diversity Calculation
- CLUMPHAP 1.1 – Haplotype-based Association Analysis
- FUGUE 0.2.3 – Haplotype Frequency Estimation
- MACH 1.0 – Haplotyping, Genotype Imputation & Disease Association Analysis
- PhyloPed 0.4 – Haplotype Inference in Pedigrees
- HaploPowerCalc 1.0 – Haplotype Estimation
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