Genotype
- PedigreeSim – Simulation of Genotypes in Pedigrees of Diploid and Tetraploid Species
- COLONY 2.0.4.0 – Parentage and Sibship Inference from Multilocus Genotype data
- LDMgen – LD Mapping with Genotype Data
- MaCH-Admix 2.0.198 – Genotype Imputation for Admixed Populations or with Large Reference Panels
- HIBAG 0.9.4 – HLA Genotype Imputation with Attribute Bagging
- SimPed – Generate Haplotype and Genotype data for Pedigree Structures
- ADMIXMAP 3.8.3103 – Model Admixture using Marker Genotype data
- SIMULATE – Simulate Genotypes in Family Members
- HIBAG 0.9.4 – HLA Genotype Imputation with Attribute Bagging
- CHIAMANTE 1.0.0 – Joint Genotype Calling algorithm for Array and Sequence data
- PHASEBOOK 2.4 – Phasing Marker Genotypes using familial (LINKPHASE), population information
- vntrTest 0.52 – Assess Association of VNTR Fragment Length Genotypes
- PedPhase 3.0 – Haplotype Inference from Genotypes on Pedigree data
- Evoker 2.2 – Graphical Tool for Visualising Genotype Intensity data
- Flapjack 1.12.05.25 – Graphical Genotype Visualization
- Admixture 1.22 – Maximum Likelihood Estimation of Individual Ancestry based on Multilocus SNP Genotypes
- bam2mpg 0.5061 – Bayesian Genotype Caller for NextGen Sequencing Data
- Structure 2.3.4 – Use Multi-locus Genotype Data to Investigate Population Structure
- MutaGeneSys 20071020 – Use Genome-wide Genotype Data to Estimate Individual Disease
- PICA 1.0.1 – Genotype-phenotype data Mining software
- VITESSE – Rapid exact Multilocus Linkage Analysis via Genotype set-recoding and Fuzzy Inheritance
- WHICHPARENTS 1.0 – Use Mutlilocus Genotype data to Determine the Most likely Parents of Offspring
- WHICHLOCI 1.0 – Use Genotype data to Identify the loci most useful for Population Assignment
- ggs – Grid Genotype Simulator
- neighborjoin / genostat/ haplostat – Explore Disease Susceptibility Prediction on Genotype/Haplotype data
- MdrPDT 2.0.1.21 – Multifactor Dimensionality Reduction and genotype Pedigree Disequilibrium Test
- MGA-SIMULATE – Simulation of Genotypes and Quantiative Phenotyps
- MouseDivGeno 1.0.4 – Genotype the Mouse Diversity Genotyping Array
- cnvHiTSeq – Detect and Genotype CNVs in WGS data
- IGG 3.0 – Integrate Genotypes for genome-wide Genetic studies
- HaploRec 2.3 – Haplotype Population-based Genotype data
- HW-QuickCheck 20061121 – Check Genotypes for Agreement with Hardy-Weinberg Expectations.
- SXTestPlate 1.0.0 – Analyses Genotypes of a SNPlex™ Control Plate
- SGCaller – Call Genotypes in Sequencing Traces
- DRBTool – Determine HLA Genotypes at the DRB1 locus
- GIST 0.3 – Detect Association between Marker Genotypes and IBD sharing at the same locus
- Margarita – Infer Genealogies from Population Genotype data
- g2h.pl / h2g.pl / h2h.pl – Convert Genotypes/Haplotypes File
- dose2geno – Generate Best Guess Genotypes from Dosage and Info File
- CalcMatch 1.12 – Concordance between two sets of Genotype data
- CNGen 1.0.1 – Convert Integrated SNP and CNV Calls into Phased Copy Number Genotypes
- GBIRP – Genotype-Based Identification of Relative Pairs
- seqEM 1.0 – Genotype Calling Algorithm for Resequencing Data
- SIMLAPLOT 1.0 – Visualize Genotype and Phenotype Relationship
- CHIAMO 0.2.1 – Genotype Calling Algorithm for Multi-cohort Study
- CNVEM 0.710 – Infer Carrier Status of CNVs in Large Samples from SNP Genotyping Data
- GSM 0.3 – Genotype-based Matching
- MicroMerge 2.0 – Merge Microsatellite Genotype Data Sets
- HAPSIM – Produce the Case-control Multilocus Genotype Data
- NNPERM 1.3 – Analyse Case-control Multi-locus Genotype Data
- GEST98 – Analysis of Genotype x Environment Interaction
- Haplotyper 1.0 – Genotype Format Data from an Excel File to a Format of Arlequin
- GeneSeq 1.0 – LD-based Genotype Calling from Shotgun Sequencing Reads
- GEDI 1.03 – Genotype Error Detection & Imputation
- ENT 1.0.2 – Genotype Phasing by Entropy Minimization
- GEVALT 2.0 – Genotype Analysis
- HaploPool – Estimate Haplotype Frequencies from Genotypes / DNA Pools
- fastPHASE 1.4.0 – Haplotype Reconstruction & Estimating Missing Genotypes
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