Posts
- Category: Genetics & Pedigree (continued)
- GENE EXPRESSION HERITABILITY 201304- Caculate Gene Expression Heritablity
- Gene Locater - Genetic Linkage Analysis software using Three-point Testcross
- Gene Stacker 1.9 - Marker-assisted Gene Pyramiding
- Gene-environment interactions - GWAS Analysis of Gene-environnement Interactions
- GeneArtisan 1.1 - Simulation of Markers in Case-Control Study Designs
- GeneCards 5.1 - Human Gene Compendium
- GeneClass 2.0.g - Genetic Assignment and First-Generation Migrant Detection
- GENECLUSTER 1.0.0 - Location and Detection of Unobserved Causal Loci
- GENECODIS 3 - Modular and Singular Enrichment Analysis for Functional Genomics
- GENECOUNTING 2.2 - Gene-counting for Haplotype analysis
- GeneFAS - Gene Function Prediction
- GeneFinder 1.2.7 - Linkage Analysis with a Variety of Extensions
- GENEHUNTER-IMPRINTING 2.1r3 / GENEHUNTER-MODSCORE 3.0 / GENEHUNTER-TWOLOCUS 1.3 - Modification of the GENEHUNTER
- GENEHUNTER++sad - Modification of Genehunter to allow for the Sad score
- Geneland 4.0.6 - Statistical Analysis of Population Genetics data
- GeneLoc 4.8 - Exon-based Integration of Human Genome Maps
- genePed 2.0 - Gene Genealogy Simulator based on Organismal Pedigree
- Genepop 4.5 - Population Genetics Software Package
- GENERATOR 1.02b - Evaluate and Group Incoherently Annotated Genes into Subsets
- GeneSeq 1.0 - LD-based Genotype Calling from Shotgun Sequencing Reads
- GeneSetScan 0.021 beta - Scan Genome-wide SNP data for Gene-set Association Analysis
- GeneTerm Linker - Functional Analysis beyond Enrichment
- GeneticDistances 20090824 - Calculate common Genetic Distances for Allele Frequency data
- Genetix 4.05 - Set of Population Genetics Programs
- Genetranassoc 1.0 - Compute Association between Genome Loci and Expression Genetic Data
- GeneViewer v.1 - View Genes and Features along a Sequences
- GenGen 1.0.1 - Pathway-based Association Tests
- Genie 2.7.2.1 - Analyze Association and Transmission Disequilibrium (TDT)
- genio 1.0.12 - Genetics Input/Output Functions
- genoCN 1.09 - Identify Copy Number States and Genotype Calls.
- GenoExp v1 - Gene Expression Prediction from Genotype
- Genoinfer 0.4 - Genotype Inference
- genomation 0.99.7 - R package for Graphics and Operations for Genomic
- Genome MuSiC 0.401 - Mutational Significance In Cancer package
- Genome-wide Evaluation - Performs Genome-wide Evaluation
- GenomeGems 3.0 - Evaluation of Genetic Variability from Deep Sequencing Data
- GenomeLaser - Haplotyping from Pedigree Genotypes
- GENOMEPOP 2.7.7.1 - Evolve Populations of Genomes under complex Evolution Models and Demography
- genomeSIMLA 1.1.3 - Forward-time Population Simulation
- GenometriCorr 1.1.22 - Spatial Correlation of Genome-wide Interval datasets
- GenomeVX - Bioinformatics Solution towards the field of Genomics
- Genomizer 1.2.0 - Analysis of Genome Wide Association Experiments
- Genonets 201805 - Analysis and Visualization of Genotype Networks
- GenoPlast 1.0 - Bayesian Analysis of Genome Plasticity
- GenoPlayer 20070621 - Visualizing and Querying Genetic Data
- GenoProof 3.0.7 - Kinship Cases and Population Studies
- GenoQuickSim 20100309 - Simulates Genotypic data using Coalescent Methods
- GENOSIM v4 - Simulate Genotypes, Breeding Values, and Phenotypes
- GenoSNP 1.3 - SNP Genotyping
- GenotypeChecker 1.005 - Checking the Inheritance Consistency of Pedigree/Genotype Data
- GenotypeViewer 20070601 - Depicts Summary Statistics for a GENEPOP file
- Genovar 0.951b - Detection and Visualization Tool for Genomic Variants
- GenoWAP 1.2.1 - Genome-Wide Association Prioritizer
- Geppetto - Population Synthesis Software
- GERMLINE 1.5.1 - Discovery Long Shared Segments of Identity by Descent (IBD) in large populations
- gespeR 0.99.5 - Gene Specific Phenotype Estimator
- GEST98 - Analysis of Genotype x Environment Interaction
- GESTALT v1.0 - Genome Editing of Synthetic Target Arrays for Lineage Tracing
- GESTE 2.0 - GEnetic STructure inference based on genetic and Environmental data
- GEVALT 2.0 - Genotype Analysis
- GFam 1.4 - Gene Family Annotation & Maintenance
- GFold 1.1.4 - Generalized fold change for Rank Differentially Expressed Genes from RNA-seq data
- ggbio 1.40.0 - Extending the Grammar of Graphics for Genomic Data
- GGD-Lasso - Graph-regularized dual Lasso for robust eQTL mapping
- gGranger 1.0.0 - Identification of Granger Causality between Gene Sets
- GGT 2.0 - Visualization & Analysis of Molecular Marker Data
- GGV / PlasmoView - The Global Genomic Visualiser
- GHap 2.0.0 - Genome-Wide Haplotyping
- gHKA - Genomic Hudson-Kreitman-Aguade test
- GHMM 0.9 - General Hidden Markov Model library
- GHOST 0.2.4 - Family-based Imputation and Association analysis
- GibbsILR - Motif-finder that optimizes for the incomplete likelihood ratio (ILR)
- GIGI 1.06.1 - Genotype Imputation Given Inheritance
- GIGI-Check 1.06 - Detection of Mendelian Consistent Genotyping Errors
- GIGI-Pick 1.06 - Subject Selection for Sequencing in Pedigrees
- Gimlet 1.3.3 - Analysing Genetic Individual Identification data
- GIMSAN 20100830 - Web-server tool for de novo Motif discovery
- GINDEL 201601 - Deletion and Insertion Genotype Calling
- Ginkgo - Cloud-based Single-cell Copy-number Variation Analysis tool
- GIPS 1.7 - Gene Identification via Phenotype Sequencing
- GIST 0.3 - Detect Association between Marker Genotypes and IBD sharing at the same locus
- GISTIC 2.0.23 – Detect Regions of Significant Copy-number Gains and Losses
- GKW 1 - Generalized Kruskal-Wallis test Incorporating Group Uncertainty
- GLaD - A Mixed-Membership Model for Heterogenous Tumor Subtype Classification
- glad - Gene Length Bias Detection in GWAS Datasets
- GLASCOW - Haplotype-based Association Mapping for Binary Traits in Structured Populations
- GLIDE 0.1 - GPU-based Linear Regression for Detection of Epistasis
- GLUE - Libraries Comprising a Random Sampling of equally probable Variants
- GMDR 1.0 - Detect Gene-by-Gene and Gene-by-Environment Interactions
- GMFilter 1.0.0 - Improves GeneMapper Analysis by removing bad wells
- GMI 1.5 - Genetic Map Interpolator
- GMM - Detects Copy Number Variation from the Distribution of Copy Number Ratios
- GNAT 1.22 - Gene / Protein Named Entity Recognition and Normalization software
- GO4J 1.1 - A Set of API used to Manipulate Gene Ontology Vocabulary
- GOBU 20200416 - Gene Ontology Browsing Utility
- goeBURST 1.2.1 - Global Optimal eBURST
- GOFFA - Gene Ontology for Functional Analysis
- GoFish 1.11alpha - Find Genes with Combinations of Gene Ontology Attributes
- GOLD 1.1.0 - Graphical Overview of Linkage Disequilibrium
- GOMI - Prediction of Indian Goat Breeds
- GONe 1.03 - Estimating Effective size (Ne) in Populations with Overlapping Generations
- Gowinda 1.12 - Gene Ontology term enrichment for Genome Wide Association Studies
- gowinda 1.12 - Gene Ontology Term Enrichment for Genome Wide Association Studies
- GP 0.26 / Arka 0.11 - Sequence Manipulation tools
- GPA 1.1.0 - Genetic analysis incorporating Pleiotropy and Annotation
- GPASS 1.0 - Genome-wide Poisson Approximation for Statistical Significance
- GPC - Genetic Power Calculator
- GPHMM 1.4 - Unravel Tangled Genotyping Data generated from Tumor Samples
- GPMAP - Global Haplotype Partitioning for Maximal Associated SNP Pairs
- GPSy - Gene Prioritization System for Conserved Biological Processes
- GPU3SNP 2.0 - Exhaustive search for Third Order Epistatic Interactions using CUDA
- GPViz 1.2.8 - Dynamic Gene-centered Visualization of Genomic Regions and/or Variants
- GRAIL / VIZ-GRAIL - Gene Relationships Across Implicated Loci
- GRAMA 1.1 - Genetic Recombinant Analysis & Mapping Assistant
- GraphIBD 0.1.0 - Fast IBD Association Testing given Genome-wide SNP data
- GrASP 0.6 beta - Graphical Assessment of Sliding P-values
- GREAM - Genomic Repeat Element Analyzer for Mammals
- GREGOR 1.4.0 - Evaluating Enrichment of Any set of Genetic Variants with any set of Regulatory Features
- GREVE - Identification of Patterns across Individual Cancer Samples
- GROK 1.1.1 - Genomic Region Operation Toolkit
- Grouped FDR - Grouped False Discovery Rate
- GRR 1.2.1.41 - Detect Pedigree Errors
- gs 2.0 - Generating Samples for Association Studies based on HapMap data
- GS3 2.2.3 - Estimates Fixed and Random Effects, Breeding Values and SNP effects for Genomic Selection
- GSA-SNP 20130719 - Process SNP data as well as Gene and Haplotype data
- GSAA 2.0 / GSAA-SNP / GSAA-Seq - Gene Set Association Analysis / Analysis-SNP / for RNA-Seq
- GSCA 2.0 - Gene Set Context Analysis
- GSDCA - Gene Set Differential Coordination Analysis
- GSdesign 0.2 - Breeding program Design with Genomic Selection
- GSM 0.3 - Genotype-based Matching
- GSMA 1.1 - Implementation of the Genome Search Meta-analysis Method
- gTDT 0.01 - A group-wise TDT for Haplotype-based Association Testing of Rare Variants with complex Disease
- GUESS 1.1 - Graphical processing Unit Evolutionary Stochastic Search
- GUniFrac 1.3 - Generalized UniFrac Distances
- GVCBLUP 3.9 / GVCeasy 1.3 - Genomic Prediction and Variance Component Estimation
- GVCHAP 2.1 - Genomic Prediction and Variance Component Estimation Using Haplotypes and SNP Markers
- GWApower 1.1 - Assess Power of Genome-wide Association Studies
- GWAS GUI 0.0.3 - Graphical Overview of your own Whole-genome Assocation study
- GWAS Pathway Identifier 1.0.0 - Pathway- and Protein-Interaction-Based Identification of Disease Specific SNP Sets in GWAS
- GWAS-NR 2.0 - noise-reduction GWAS analysis
- GWAS4D - Multidimensional Analysis of Context-specific Regulatory Variant for Human Complex Diseases and Traits
- GWASelect 1.0 - Variable Selection Method for Genomewide Association Studies
- GWAsimulator 2.1 - Rapid Whole Genome Simulation program
- GWAtoolbox 2.2.4-7 - Quality Control and Handling of Genome-wide Association Studies Meta-analysis data
- GWiS 1.1 - a Gene-based Test of Association
- GxEscanR 2.0.2 - Detect GxE interactions in a Genome-wide Association Study
- H-Clust - Tag SNP Selection
- H2boot beta - Program for Bootstrap Estimates of Quantitative Genetic Data
- HaDiT 20090702 - Computing and Visualizing Allelic Distortion in Tumor SNP data
- HAP 0.2.1 - Haplotype Analysis of Polymorphic Markers
- hap-ibd - Detect Identity-by-descent Segments
- HAPAA 1.0 - HMM-based Analysis of Polymorphisms in Admixed Ancestries
- HAPAL - Mapping HAPlotype-haplotype Interactions with Adaptive Lasso
- HAPAR - Haplotype Inference by Parsimony
- hapassoc 1.2-8 - Inference of Trait Associations with SNP Haplotypes and other attributes using the EM Algorithm
- HapBound / SHRUB - Detecting Crossover Recombination
- HapBound-GC and SHRUB-GC - Detect Crossover and Gene-Conversion Recombinations
- hapCART - Detect Interactions among Haplotypes in Association with a Disease
- HapEvolution - Detect Gene-gene Interactions from Case-control Haplotype data
- HapFABIA 1.28.0 - Identification of very short Segments of IBD Characterized by Rare Variants
- HapFinder 1.0 - Finding common Haplotype Blocks in a database
- hapFLK 1.2.1 - Detection of Selection Signatures based on Multiple Population Genotyping data
- HapFlow 1.1.2 - Visualising Haplotypes in Sequencing Data
- HapForest - Forest for Detecting Haplotypes and Interactions
- HAPGEN 2.2.0 - Simulate Case Control Datasets at SNP Markers
- Hapi 1.03 - Rapid Haplotype Inference for Nuclear Families
- HAPI-UR 1.01 - HAPlotype Inference for UnRelated samples
- Haplo Stats 1.8.6 - Statistical Methods for Haplotypes When Linkage Phase is Ambiguous
- HAPLO-IHP - Haplotype Inference using Identified Haplotype Patterns
- HaploBlock 1.2 - Haplotype Block Identification and Resolution for High-density SNP data.
- Haploclusters - Detect Excess Haplotypes Sharing
- haploconfig 1.1 - Implementing the Simulation-based Haplotype Configuration Test
- HaploGeneMapper 1.0 - Genomic Proximity of Haplo Insufficient Genes Visualization tool
- HaploHMM 20140622 - Hidden Markov Model (HMM) Based Program for Haplotype Inference
- HaploPainter 1.043 - Pedigree and Haploytype Drawing Tool
- HaploParser 0.1 - Haplotype Inference using Combinatoric Parsing
- HaploPOP 1.0 - Build Haplotypes for Population Genetic Structure Inference
- HaploPowerCalc 1.0 - Haplotype Estimation
- HaploPS 1.0 - Identifying recent Positive Selection Signals in the human Population
- HaploRec 2.3 - Haplotype Population-based Genotype data
- Haploscope - Visualize Haplotype Diversity
- Haploscribe 0.1.0 - Chromosomal Haplotypes by Genetic Phasing of Human Families
- HaploShare 1.02 - Find Shared Haplotypes among Patients from a common recent Ancestor
- Haplosuite 1.1 - R package for Haplotype Clustering and Visualization
- HAPLOT 3.2 - Graphical Presentation of Haplotype Block Structures
- Haplotype meta-analysis - Meta-analysis of Haplotype Association Studies
- Haploview 4.2 - Analysis & Visualization of LD & Haplotype Maps
- HaploVisual 0.04 - Haplotype data Visualization and Analyzation
- haploxt 1.08 - LD Calculator from Phased Haplotypes
- HapMap filter 1.0 - Preprocess the HapMap Genotypic data for Association Studies
- HapMDR - Detection of Haplotype-haplotype Interaction
- HapMiner 1.1 - Haplotype-based Linkage Disequilibrium mapping via direct Data Mining
- HAPMIX v2 - Identify Ancestry Segment
- HAPMIXMAP 1.0 - Model HapMap Haplotypes
- HapMuC 1.0 - Somatic Mutation Caller
- HAPPY - Haplotype Scoring for Generalized Linear Modeling and Haplotype-Disease Association Tests
- HAPPY 1.2 - Reconstruct HAPlotYpes
- hapQTL 0.99 - Haplotype Quantitative Loci
- HAPredictor - Gene-specific method for Predicting Hemophilia-causing Point Mutation
- Hapsample 0.12 - Association Simulator for Candidate Regions or Genome Scans
- HapSeq 2 - Genotype Calling and Phasing for WGS data
- HAPSIM - Produce the Case-control Multilocus Genotype Data
- HapSim 0.31 - Haplotype Data Simulation
- HAPSIMU 1.0 - Genetic Simulation Platform based on real Haplotype Data
- HAPSTAT 3.0 - Statistical Analysis of Haplotype-disease Association
- HapTagger - Tag SNP Selection Using Haplotype
- HapTree 1.0 - Polyploid Haplotype Assembly tool
- HapYDive - Excel Plugin for Y-STR Haplotype Diversity Calculation
- HARE - Harmonizing Genetic Ancestry and self-identified Race/Ethnicity
- harp 20140925 - Haplotype Analysis of Reads in Pools
- HARSH 0.21 - Haplotype Inference using Reference and Sequencing Data
- HCGene 1.0.1 - Hierarchical Classification of Genes
- HCMV / MRA - Drug / Mutation Resistance Mutations
- HDBIG - High Dimensional Brain Imaging Genomics
- HeatMapper 1.1 - Draws Heatmaps and Displays Clinical data next to the Heatmap
- HEIDI 0.1 - Partition the total Heritability into the Contributions of Genomic Regions
- Heinz 2.0 / xHeinz 1.2 - Single / Cross-species Module Discovery
- Helium 190903 – Helium Pedigree Visualization Framework
- Heritability Calculator - Compute Heritability for different Genetic Architectures
- Heu-MCHC 1.0.2 - Heuristic Algorithm for the Haplotype Inference problem on Pedigree data with recombinations and mutations
- HGT - Simulate and Estimate Horizontal Gene Transfer events
- hgvs 1.5.1 - Tools to Parse, Format, and Map Biological Sequence Variants
- HIBAG 1.28.0 – HLA Genotype Imputation with Attribute Bagging
- Hickory 1.1 - Analysis of Geographic Structure in Genetic data
- HiDe 20120609 - Infer Highways of Horizontal Gene Transfer in the Evolutionary History of a set of Species
- HIERFSTAT 0.5-10 - Package for R to Compute & Test Hierarchical F-statistics
- HighMap - Construction and Analysis of High-density Linkage Map
- HilbertVis 1.51.0 - Visualization of Genomic data with the Hilbert curve
- hindex 1.42 - Calculates a Hybrid Index for Individuals of unknown Ancestry
- HIPPO 1.0/ AEML 1.0 - Estimate Population Haplotype Frequencies from Pooled SNP data
- HIT 1.0.1 - Haplotype Inference Technique
- HiTSelect 20140708 - High-throughput Genome Wide Screen Deconvolution Software
- HIVE Genecast 0.3.0 - Human Gene Variation Information for Mobile Devices
- HKA 20100709 - Statistical Test for Natural Selection
- HM-Net - Bayesian model for Histone Modifications
- HMC 0.9.1 - Haplotype Inference tool based on Markov Chain model
- HMMvar 1.1.0 / HMMvar-multi / HMMvar-func - Functional Effects of Variants in Coding Regions
- HMS 0.1 - Hybrid Motif Sampler
- HomeoSplitter 1.01 - Disentangling Homeologous Contigs in Allo-tetraploid Assembly
- HOMOG - Homogeneity Test
- HotSpot3D 1.8.0 - 3D Hotspot Mutation Proximity Analysis tool
- HotspotFisher - Detect Recombination Hotspots from Population Polymorphism data
- HOTSPOTTER 1.2.1 - Identify Recombination Hotspots
- HP-Rare 20090202 - Rarefaction of Private Alleles and Hierarchical Sampling Designs
- HPlus 4.0 - Haplotype Analysis
- HPM / TreeDT - Association Analysis using Haplotype data or Genotype data
- HREfinder 1.0 - Detection of Homologous Recombination Events from SNP data
- HRRA - Homozygous Regions of Recent Ancestry
- HRSS 0.2 - Hybrid Relative Specificity Similarity based on Gene Ontology
- HS - A new index of Host Specificity
- HS-TDT - Haplotype Sharing Transmission Disequilibrium Test
- hsphase - Pedigree Reconstruction, Detection of Recombination Events, Phasing and Imputation of half-sib Family Group
- HTR - Haplotype Trend Regression
- HTreeQA 1.0 - using semi-perfect Phylogeny Trees in Quantitative Trait loci study on Genotype data
- HTSmix 1.0 - Interpretation of High-throughput Perturbation Screens with Low-dimensional Phenotypes
- HW-QuickCheck 20061121 - Check Genotypes for Agreement with Hardy-Weinberg Expectations.
- hwdglm 1.0 - Testing Hardy-Weinberg Disequilibrium Using Generalized Linear Model
- hweStrata 1.0 - Exact Stratified Test for Hardy-Weinberg Equilibrium
- HybridCheck v1.0.1 - Hybridisation Recombination and Introgression Detection and Dating
- HyDRA - Hybrid Distance-Score Rank Aggregation software for Gene Prioritization
- HyLiTE 2.0.2 - Analyzes Transcriptome data from Allopolyploid Species
- HyperLasso - Simultaneous analysis of GWAs
- hypred 0.5 - Simulation of Genomic Data in Applied Genetics
- hzAnalyzer 0.2.0 - Detection and Analysis of Contiguous Homozygosity in High-density Genotyping Datasets
- i-GSEA4GWAS 1.1 - Improved-Gene Set Enrichment Analysis for Genome-Wide Association Study
- iAdmix 1.0 - Using population allele frequencies for Computing Individual Admixture Estimates
- IBDfinder 20121128 - Visual display of homozygous regions in SNP data files
- IBDmap - Identical by Descent Mapping
- IBDmut - Infer Mutation and Gene Conversion Rates using Identical-by-descent Segments
- IBDNe 20200423 - Estimate Effective Population size in recent Generations
- IBDseq - Detect IBD Segments using Allele Frequencies
- IBDSim 2.0 - Simulation of Genotypic data under general Isolation by Distance models
- iCAGES 1.0.2 - Prioritizing Cancer driver Genes
- ICDMR - Identification of Consistently Differentially Methylated Regions
- ICSNPathway 1.1 - Identify Candidate Causal SNPs and Pathways from Genome-wide Association Study
- IdCheck 1.0.0 - a Tool for Genotype and Gene Expression Sample Identity Checking
- IdeogramBrowser 0.20.4 - Visualization of Genomic Aberrations using Affymetrix SNP Arrays
- IDP 0.1.10/ IDP-fusion v1.1.2 - Gene Isoform Detection and Prediction tool
- iECAT 0.8 - Integrating External Controls into Association Test
- IGB 0.01 - Computing Individualized Genetic Barrier
- IgC2N - Identification of Germline Changes in Copy Number
- IGG 3.0 - Integrate Genotypes for genome-wide Genetic studies
- iHS_calc 1.4 - Calculate the Integrated Hapotype Score
- Illuminus - Genotype Calling algorithm
- ILPMap 20110128 - Construct Consensus Genetic Maps under Comparative Analysis
- IMa3 v1.12 - Generate Posterior Probabilities for complex Demographic Population Genetic Models
- iMAAPs - Infer multiple-wave Admixture by fitting ALD using a p-spectrum
- imapping - Likelihood Ratio Test process for QTL Detection
- imappingfamily - QTL Detection in a Population with Family Structure
- IMIG - Infer Recent Migration rates from Individual Genotypes
- Immanc 5.0 - Detecting Immigrants Using Multilocus Genotypes
- IMPUTE 5 v1.1.5- Genotype Imputation in Genome-wide Association Study
- indel-Seq-Gen 2.1.03 - Simulates highly Divergent DNA sequences and Protein superfamilies
- INDELible 1.03 - A powerful and flexible Simulator of Biological Evolution
- InferRho 1.0 - Recombination Rate Inference
- infocalc 1.1 - Measure the Ancestry Information Content of Genetic Markers
- inPHAP 1.1 - Interactive Phased Haplotype Visualization
- INPower 0.0.1 - Estimating the number of Susceptibility SNPs and Power of Future studies
- INRICH 1.1 - Interval-based Enrichment Analysis Tool for Genome Wide Association Studies
- InSNP 1.0 - Detect Substitution and Indel SNPs in Sequencing Traces
- Int-Path - Causal Gene Identification and Gene Regulatory Pathway Inference
- intcomp 0.3.30 - integrative Cancer Gene Detection algorithms
- introgress 1.23 - Mapping Components of Isolation in Hybrids
- invertFREGENE - Simulate Sequence Level data with Inversions
- IPGWAS 3.4 - Integrated Pipeline for Genome-Wide Association Studies
- IPHULA / pIPHULA 1.16 - Inference of Population History Using a Likelihood Approach
- IPred 201409 - Integrate ab initio and evidence based Gene Predictions
- IQLS 1.2 - Haplotype Analysis for Case-Control Samples with Related Individuals
- iQTL-F2 - Mapping imprinted Quantitative Trait Loci (iQTL) in F2 Experimental Cross
- iQTL-VC - iQTL mapping with Variance Component mode
- IRILmap 1.1 - Linkage Map Distance Sonversion software
- IRiS - Identification of Recombinations in Sequences
- IrisPlex and HIrisPlex Eye and Hair Colour DNA Phenotyping Webtool
- ISCA 0.1.8 / ISCA plotter 120904 - Inheritance State Consistency Analysis
- IsoEM 2.0.0 - Inferring Alternative Splicing Isoform Frequencies from High-Throughput RNA-Seq Data
- isoscatR / scatR - Spatial Assignment using Genetic and Isotopic data
- ISS - In-silico Gene Sequencing Method
- iXora - Exact Haplotype Inferencing and Trait Association
- J/qtl 1.3.4 - Java GUI for R/qtl
- Jack the Knife 1.0 - Estimate the Significance of Traits
- JAG 1.1 - Gene-set Analysis in GWAS Datasets
- JAMP 1.0 - multivariate GWAS Analysis
- Jannovar 0.36 - A Java library for Exome Annotation
- JAWAMix5 r2 - HDF5 based JAva implementation of Whole Genome Association Studies using Mixed models
- JCat 1.0 - Java Codon Adaptation Tool
- JEPEG 0.2.0 / JEPEGMIX 0.1.0 - Joint Effect on Phenotype of eQTLs/functional SNPs associated with a Gene
- JISTIC - Identify Driver Aberrations in Cancer
- JLIN 1.6.0 - Visualisation of LD Analysis
- JMATING 1.0.8 - Analysis of Sexual Selection and Sexual Isolation Effects from Mating Frequency data
- JMS v1 - Evaluation of Diagnostic Status of Juxtaposed Microsatellite Systems
- JODA 1.33.0 - Quantifying Gene Deregulation using Knowledge
- JOINMAP 4.1 - Calculation of Genetic Linkage Maps
- jointSeg 0.7.0- Joint segmentation of multivariate (copy number) signals
- JointSLM 0.1 - Detect Recurrent Copy Number Variations in Depth of Coverage data
- jPopGen 1.0b7 - Collection of Java programs for Population Genetic Analysis
- Kafeen 2.1.0 - Querying Genetic Variation data from database
- Kaviar 160204- Queryable database of known Variants
- KBAT 1.2 - Genome-wide and Candiate-region Association Mapping
- kcoeff - Calculate Genetic Relatedness from SNP data
- KELVIN 2.7.0-a2 - Statistical Genetics software package in support of the PPL Statistical Framework
- Kelviz v3.3.1 - Plot and Annotate Genetic data analysis results
- kGEM 0.7 / ERIF 1.0 - Reconstructing a Viral population from Single-Amplicon reads
- KGG 4.1 - Knowledge-based mining system for Genome-wide Genetic studies
- KGGSeq 1.2 - Genomic and Genetic studies using Sequence data
- KimTree 2.0.1 - Inferring Population Histories using Genome-wide Allele Frequency data
- KIN - Kinship Calculator
- KinCohort - Likelihood-based analysis of Kin-cohort data
- KING 1.4 - Identify Family and Population Structure
- KinInbcoef 1.1 - Calculation of Kinship and Inbreeding Coefficients
- KinInbcoefX 2.0 - Calculation of X-chromosome Kinship Coefficients
- KinInfor v1 - Calculate Informativeness of Markers in Inferring Pairwise Relatedness
- kinship2 1.8.5 - Pedigree Functions
- KSimPop 2.1 - Build Biological Populational Model
- LadderFinder 0.1.0 - Solve Problem in DNA Genotyping
- LAMP 0.0.12 - Linkage & Association Modeling for Pedigrees
- LAMP 2.5 / LAMP-LD 1.1 - Estimate Locus Specific Ancestry
- LAMPLINK v1.12 - Detection of Statistically Significant Epistatic Interactions
- Lanc-CSV 0.1 - Local Ancestry Inference using Continental Specific Variants
- LAPD - Estimate Maximum Likelihood Allele and two-locus Haplotype Frequencies
- LAPSTRUCT 1.0 - Geometric Approach to Describe Population Structure
- LASER 2.04 - Locating Ancestry using SEquencing Reads
- LBL 1.0 / LBLGXE 1.3 - Bayesian Lasso for detecting Rare Haplotype-Environment Interaction
- LCMT - Multiple Genetic Markers Association test
- LD Select 1.13 - Patterns of Linkage Disequilibrium Analysis
- LD-Plus - Display of Single SNP Statistics in the Context of Linkage Disequilibrium and Haplotype Structures
- LDetect - Automated Analysis of Multiple Genome-wide Association Studies
- LDExplorer 1.0.3 - Whole-genome LD-based Haplotype Block Recognition
- ldgroup - Linkage Disequilibrium Grouping of SNPs
- LDhat 2.2 - Analysis of Recombination Rates from Population Genetic Data
- LDheatmap 1.0-4 - Graphical Display of Pairwise Linkage Disequilibria between SNPs
- LDhelmet 1.10 - Fine-scale Recombination Rate Estimation
- LDlink / LDlinkR 1.1.2 - Linkage Disequilibrium in Population group
- LDSO 1.02 - Linkage Disequilibrium with Several Options
- LDsplit - Association Studies of Recombination Hotspots using SNPs
- LDtests 1.0 - Tests of Linkage Disequilibrium and Hardy-Weinberg Equilibrium
- LDWP - Linked Region Detection without Pedigree
- LEA / parLEA - Likelihood-based Estimation of Admixture
- LEADMIX 1.0 - Likelihood Estimation of ADMIXture
- LFMM 1.5 - Inferring Population Genetic Structure and Gene-environment Associations
- LHiSA 20080507 - Local High-scoring Segments for Association
- LIAN 3.7 - Testing Genome-Wide Linkage Equilibrium From Multilocus Data
- LIBFBAT 0.5.1 - C++ library for Family Based Association Testing
- libsequence 1.9.8 - C++ Class Library for Population Genetics
- LIden - Linkage Analysis Software
- Ligate Haplotypes 0.04 - Ligate Haplotypes with Two Overlapping Regions
- LIME 0.2-1 - Likelihood approach for detecting Imprinting and Maternal Effects
- LineUp - Statistical Detection of Chromosomal Homology
- LINKAGE - Pedigree Linkage Analysis
- LINKMFEX 2.4 - LINKage analysis package for outcrossed families with Male Female EXchange of the mapping parent
- LINKSH - Genome-wide 2-point/m-point Linkage analyses
- linkSNPs 1.0 beta - SNP Detection and Haplotype Reconstruction
- LIPED - Program for Linkage Analysis
- LMM-Lasso - Lasso Multi-Marker Mixed Model for Association Mapping with Population Structure Correction
- LocalDiff 201309 - Characterize Non-stationary Patterns of Isolation by Distance
- LocHap 2.0 - Local-Haplotype Variant Calling Software
- LOCO-LD - LOcalization COrrected for Linkage Disequilibrium
- LocusExplorer 0.7.2 - Visualisation of Human Genetic Association data and Biological Annotations
- LOCUSMAP 2.1 - Rapid Linkage Analysis and Map Construction of Loci
- LocusTrack v1 - Integrated Visualisation of GWAS Results and Genomic Annotation
- LocusView 2.0 - Generate Images of Chromosomal Regions
- lodGWAS 1.0-7 - Genome-Wide Association Analysis of a Biomarker Accounting for Limit of Detection
- LOHAS 2.3 - Loss-of-heterozygosity Analysis Suite
- Loki 2.4.5 - Monte Carlo analysis of multiple QTL
- LOLA 1.24.0 / LOLAweb - Genomic Locus Overlap Enrichment Analysis
- LORS - LOw-Rank Representation and Sparse Regression for eQTL mapping
- LOT 1.2 - Linkage Analysis of Ordinal Traits
- LPmerge 1.7 - Merging Linkage Maps by Linear programming
- LPPH - Perfect Phylogeny Haplotyping
- LRASSOC 1.1 - Analysis of Case-control Data for Diseases with Two Susceptiblity Loci
- LRTag - Select SNP Markers across Multiple Populations
- LSKM 1.0 - Multilocus Association Test for Quantitative Traits
- LSR - Estimate Region-specific p-values in Genetic Association Mapping studies
- LTSOFT 3.0 - Analysis of Case-control Association Studies with known Risk Variants
- LUCA 1.0-6 - Likelihood Under Covariate Assumptions
- MACH 1.0 - Haplotyping, Genotype Imputation & Disease Association Analysis
- MaCH-Admix 2.0.203 - Genotype Imputation for Admixed Populations or with Large Reference Panels
- mach2dat 1.0.24 - Imputation-based Analysis of Binary Traits
- mach2qtl 1.13 - Imputation-based Analysis of Quantitative Traits
- MACLEAPS 1.0.2 - Machine Learning Analysis Pipeline for Genome-Wide Accociation Study SNP data
- MACOED - Multi-objective Heuristic Optimization Methodology
- Madeline 2.0 - Pedigree Drawing Engine
- MADGiC 0.2 - a Model-based approach for identifying Driver Genes in Cancer
- MAESTRO 1.2.35 / MAESTROweb - Multi Agent Stability Prediction upon point Mutations
- MAFsnp 1.0 - SNP Caller Using Next-Generation Sequencing Data
- MAGENTA 2.4 - Meta-Analysis Gene-set Enrichment of variaNT Associations
- MAGI - Mutation Annotation & Genome Interpretation
- MAGMA 1.1 - Multiobjective Analyzer for Genetic Marker Acquisition
- Magnolya 0.15 - Detection of Copy Number Variation
- MAGprediction - Gene Allele Prediction Using Unphased SNP data
- MAIA 1.0 - Complex Segregaton Analysis in Animal Pedigrees
- MALDSoft 1.0 - Admixture Mapping of Complex Trait Loci
- Malin 20080413 - Analysis of Eukaryotic Gene Structure Evolution
- MamPhEA - Mammalian Phenotype Enrichment Analysis
- MAN-A1 - Complex Segregation Analysis in Humans
- MANTEL-STRUCT 1.0 - Tests for Population Structure through the use of Mantel Tests
- MANVa 0.982b - Multilocus Analysis of Nucleotide Variation
- MAOS 1.2 - Meta-Analysis with Overlapping Subjects
- MapChart 2.2 - Graphical Presentation of Linkage Maps and QTLs
- MAPDISTO 1.8.1 - Map Genetic Markers in Experimental Segregating Populations Like Backcross
- MapDraw 2.1 - Excel Macro for Drawing Genetic Linkage Maps
- MapInspect - Compare & Display Linkage Maps
- MAPL98 - Linkage Mapping & QTL Analysis
- MapPop 1.0 - Software for Selective Mapping and Bin Mapping
- MapQTL® 6 - Mapping of Quantitative Trait Loci in Experimental Populations of Diploid Species
- MAPS 2.0 - Mutation and Polymorphism Survey
- MareyMap 1.3.4 - Recombination Rate Estimator
- Margarita - Infer Genealogies from Population Genotype data
- MargFreq 1.02 - Calculate Marginal Frequencies at each Position of a Nucleotide/Amino Acid Sequence
- MarViN 0.1.0 - Rapid Genotype Refinement for Whole-Genome Sequencing Data using Multi-Variate Normal Distribution
- MASA 1.0.0 - Multi-threshold (and Multi-marker) Association Study Analysis
- MASS v7 - Meta-Analysis of Score Statistics
- Matapax - Genome Wide Association Study Web Platform
- Matrix eQTL 2.1.0 - Ultra fast eQTL Analysis via Large Matrix Operations
- MaxCon 1.0 - The Maximum Contribution from a sampled Ancestor Population to a more Recent Population
- maxdip - Estimating Cross-over and Gene Conversion Rates from Diploid unphased Polymorphism data
- maxhap - Estimating Cross-over and Gene Ronversion Rates from Haploid (phased) Polymorphism data
- MAXPROC - Calculate Maximum Likelihood Estimates of Linkage Parameters
- MBEToolbox 3.0 - MATLAB Molecular Biology & Evolution Toolbox
- MBMDR 4.4.1 - Model-Based Multifactor Dimensionality Reduction
- mbs 2 - Generating Samples of DNA Sequences with a Biallelic site under Selection
- MC-PDT 0.2.4 - Linkage Disequilibrium Test
- MCA 3.1 - Visualization method for Correlated Subpopulations
- MCDGPA - Modularized Candidate Disease Genes Prioritization Algorithm
- MCentridFS - Multi-class Centroid Feature Selection
- MCLEEPS 1.1 - Monte Carlo Likelihood Estimation of Effective Population Size
- MCMC++ 1.2 - C++ class library for Monte Carlo Markov Chain Analysis of Bayesian models
- MCQTL 2.0 - Multi-allelic QTL Mapping in Multicross Designs
- McSNP 1.0 - Melting Curve SNP
- MDBLOCKS 1.0 - Minimum Description length method for Haplotype BLOCKS
- MDIV - Estimate Divergence Times and Migration Rates between two Populations
- MDLBlockFinder 1.1 - Haplotype Block Identification
- MDR 3.0.2 - Multifactor Dimensionality Reduction
- MDR-Phenomics 1.0 - Detect Gene-gene Interaction in the Pedigree Data
- MdrPDT 2.0.1.21 - Multifactor Dimensionality Reduction and genotype Pedigree Disequilibrium Test
- MDSOutlier 0.04 - Whole-genome Case-control Association Analysis
- MECPM - Maximum Entropy Conditional Probability Moldeling
- MedSavant 1.3.6 - Search Engine for Genetic Variants
- MEGA-V - Mutation Enrichment Gene set Analysis of Variants
- Mega2 6.0.0 - Manipulation Environment for Genetic Analyses
- MegaMapper 1.01e - Software for Positional Cloning of Mutations by Whole Genome Sequencing
- MegaSNPHunter - Detect Disease Predisposition SNPs and High Level Interactions
- mendel-gpu - GPU enabled Haplotying and Genotype Imputation
- Mendelian - Heuristic Variant Filtering
- MendelScan 1.2.2 - Analyze Exome data for Mendelian Disorders
- MendelSoft 0.9.8 - Detect Marker Genotyping Incompatibilities
- MergeMap - Construct Accurate Consensus Genetic Map
- MERLIN 1.1.2 - Pedigree Analysis
- MerlinViewer 20101207 - Visualising Merlin output data
- META 1.7 - Carryout Meta-analysis of Genetic Studies
- metagen - Meta-analysis of Genetic association Studies
- Metal 20110325 - Meta-analysis of Genomewide Association Scans
- MetaModelManager 1.0.6 - Transdisciplinary Species Risk Assessment
- MetaPCA 0.1.4 - Meta-analysis in the Dimension Reduction of Genomic data
- MetaQTL 1.2.0 - Meta-analysis of QTL Mapping Experiments
- MetaSKAT 0.81 - Meta-analysis for multiple markers
- METASOFT 2.0.1 - Meta-analysis Tool
- Metastats - Detect Differentially Abundant Features in Metagenomic Data
- metatrend - Estimate Trends in Cumulative Meta-analysis
- MFDM 1.1 - Detect recent Positive Selection Reliably in Natural Populations
- MFG Tools - includes GenoTool, PatientTool and SampleTool
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