Posts
- Category: Genetics & Pedigree (continued)
- AlleleRetain 2.0.2 - Simulate Small Populations
- Allim 1.2 - Measuring Allele Specific Gene Expression
- ALLOY 0.2 - Ancestry Inference on Local Genomic Segments
- ALOHA 1.2 - Genome-wide Analysis of Allele Frequency
- Alohomora 0.33 - Linkage Analysis tools and Affymetrix Mapping
- AlphaAssign 1.1 - Parentage Assignment with Genotyping-by-sequencing data
- AlphaBayes - Performing Genome Wide Association Studies and Genomic Selection
- AlphaDrop beta - Simulating Sequence and SNP data, QTL effects, Pedigrees, and Breeding Values
- AlphaFamImpute 0.0.1 - Imputation in full-sib families from Genotype-by-sequencing data
- AlphaImpute 1.9.8.3 - Imputing and Phasing Genotype data in Populations
- AlphaMPSim R1 - Flexible Simulation of Multi-parent Crosses
- AlphaPeel 0.1.0 - Calling, Phasing, and Imputing Genotype and Sequence data in Pedigree Populations
- AlphaPhase 1.2 - Phasing Genotype data
- AlphaPlantImpute - Phasing and Imputing Genotype data in Plant Breeding Populations
- AlphaRecode - Recode Pedigree and Sort it
- AlphaSeqOpt - Determining Optimum Distribution of Sequencing Resources within Population of interest
- AlphaSimR 0.13.0 - Breeding Program Simulations
- AMELIA - Allele Matching Empirical Locus-specific Integrated Association test
- Ameliorator 1.0 - Calculate Amelioration Times for DNA Sequence Evolution
- AnA-FiTS 1.0.3 - Forward-in-time Simulator for Polymorphism data
- analysis 0.8.8 - Evolutionary Genetic Analysis
- ANCESTRYMAP 2.0 - Find Skews in Ancestry
- AncestryPainter v5 - Illuminate the Ancestry Compositions of Populations and Individuals
- ANGES 1.01 - Reconstructing ANcestral GEnomeS maps
- Annot 1.0 / PLINK2wakefieldBF 1.0 - Calculate Bayes Factors
- AnnotQTL 20110907 - Gather Functional and Comparative Information on a Genomic Region
- ANNOVAR 20210202 - functional ANNOtation of genetic VARiants
- AnnTools 1.1 - Annotation Toolkit for Genomic Variants
- AntMap 1.2 - Software for Constructing Genetic Linkage Maps
- API-CALC 1.0 - Calculate PIave for F-IS and F-ST
- APL 1.1 - Association in the Presence of Linkage
- APL-OSA Beta - Identify Genetically Homogenous Subset of Families
- APSampler 3.6.1 - Use Monte Carlo Markov Chain for Identifying of Genetic Background of Complex Diseases
- AQUASPLATCHE 1.1 - Simulate Genetic Diversity based on a Realistic Vectorized Environment
- Arboretum - Reconstruction and analysis of Evolutionary History of Condition-specific Transcriptional Modules
- ArchaicSeeker 2.0 - Detecting Archaic Introgression Sequences and Reconstructing Introgression History
- ARGON 0.1 - Fast Whole-genome Simulation of the discrete time Wright-Fisher Process
- ARIEL - Explore Effects of Rare Variants
- ArkMAP 2.78 - Draw and Align Genetic Maps
- Arlequin 3.5.2.2 - Population Genetics Data Analysis
- Armitage 0.02 - Armitage Trend Chi-square Statistics
- ARR 1.0 - Adaptive Ridge Regression for Rare Variant Detection
- ARTP 2.0.9.45 - Gene and Pathway p-values computed using the Adaptive Rank Truncated Product
- ASF - Two-Locus Asymptotic Sampling Formula
- ASMC - Ascertained Sequentially Markovian Coalescent
- ASP / ASPHARE - Calculator for Gene Mapping using a Sibpair Design
- ASPEX 2.5 - Affected Sib-pair Exclusion Mapping
- aSPU 1.50 - Adaptive Gene- and Pathway-Trait Association Testing with GWAS
- asSeq 0.99.2 - Statistical Framework for eQTL Mapping using RNA-seq Data
- ASSET 2.11.0 - Combined Analysis of Heterogeneous Traits and Disease Subtypes
- Assimilator 1.31 - Inform Selection of Associated Genetic Variants for Functional Studie
- ASSIsT 1.02 - Automated SNP Scoring Tool
- AsVis 20051125 - Visualizing Association Rules in SNP Neighborhoods
- ATHENA 1.1.0 - Discover Epistasis among Quantitative Trait Loci
- ATOM - Association Test via Optimally-weighted Markers
- ATRIUM 1.0 - Testing Untyped SNPs in Case-Control Association Studies with Related Individuals
- atSNP 1.1.2 - Large-scale Testing for SNP-motif Interactions
- AutocorQ - Characterise and Test the Spatial Autocorrelation of Quantitative Traits
- AUTOSCAN 1.0.3 - Easy Genome-wide Scans with Analyze
- AutoSNPa 20121128 - Visual analysis of SNP data for autozygosity Mapping
- AVIA 3 - Analysis of Genomic Variants and Genes
- BACH 1.1 - Fast Haplotype Inference via Context Tree Weighting
- BACOM 1.0 - Bayesian Analysis of COpy number Mixtures
- BACTFREQ - Maximum Likelihood Estimation of Bacterial Allele Frequencies
- BaDGE 1.1.7 - Bayesian model for Detecting Gene Environment interaction
- BAFRegress 0.9.3 - Detects and Estimates Sample Contamination using B allele frequency data
- BALD 0.2.1 - Blockwise Approach using Linkage Disequilibrium
- BALL-SNP - Combining Genetic and Structural Information to Identify Candidate Non-synonymous SNPs
- BAMA - Bayesian Analysis of Multilocus Association
- bammds 2014 - Create MDS plot of Populations for Genetic data
- bamova 1.02 - Bayesian Analysis of Molecular Variance
- BAMSE - Bayesian Association for Multiple SNP Effects
- BANANAS - Infer Population Trees based on Molecular Marker data
- BaobabLuna 1.1 beta - Manipulation of Signed Permutations in the Context of Genomic Evolution
- BARS - Bayesian Adaptive Regression Splines
- Bayenv 2.0 - Identify Loci Underlying Local Adaptation
- BayesAss 3.03 -Bayesian Inference of Recent Migration Using Multilocus Genotype
- BayesAss- 1.0 - Bayesian Population Assignment of Haploid Organisms Using Multilocus Genotypes
- BayesAssNM 1.0 - Bayesian Inference of Recent Migration Using Multilocus Genotypes (Migrants Not Included In the Sample)
- BayeScan 2.1 - Detect Natural Selection from Population-base Genetic Data
- BayesDiallel 0.982 - MCMC Sampler for Analyzing Diallel Crosses of Inbred Strains
- BAYESFST - Bayesian Estimation of Coancestry Coefficient FST
- BayesMendel 2.1-7 - R package for Mendelian Risk Prediction
- BayeSSC - Bayesian Serial SimCoal
- Baypass 2.2 - Genome-Wide Scan for Adaptive Differentiation and Association Analysis with Population-specific Covariables
- BDMC 2.1 - Maximum Likelihood Estimation of Allele Ages
- BEAGLE 5.2 - Genetic Analysis Software Package
- BEAGLE Utilities 2013 - Utility programs for Manipulating Large Data Files
- BEAGLECALL 1.0.1 - Genotype Calling using Linkage Disequilibrium for unrelated individuals
- BEAM 3 - Disease Association Mapping
- BEAMimpute - Bayesian Epistatis Association Mapping via Imputation
- BEDASSLE 1.5 - Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology
- BestRepeat 1.0 - Variance Components Linkage Analysis with Repeated Measurements
- BETASEQ 1.0 - Data Correction in Unbalanced Sequencing Studies for Valid Rare Variant Association Testing
- BhGLM 1.1.1 - Bayesian hierarchical GLMs to Genetic Data Analysis
- BHIT - SNP Interaction Detection
- BiERapp 1.4.2 - Gene/Variant Prioritization tool
- Bifido Punnett Square Calculator 4.0 final - Genetic Calculator for Predicting the Offspring Results of Genetic Crosses
- bilinear.fit 0.1 - Preform Bilinear Regression Fits to 16O/18O Isotope Labeling
- BIMBAM 1.0 - Bayesian IMputation-Based Association Mapping
- BIMr 1.0 - Bayesian Inference of imMigration rates
- BINOCh 1.0.0 - Binding Inference from Nucleosome Occupancy Changes
- BioBin 2.3.0 - Explore Rare Variant Population Stratification
- BiodivR 1.2 - Compute Statistically Unbiased Indices of Species Diversity
- Biofilter 2.4.2 - Knowledge-driven Multi-SNP analysis of large scale SNP data
- BioHEL / BioHEL RPE - Bioinformatics-oriented Hierarchical Evolutionary Learning/ Rule Post-processing Engine
- BioMercator v4.2.3 - Genetic Maps and QTL Integration
- BIOR 2.2.2 - Rapid, Flexible System for Genomic Annotation
- Birdsuite 1.5.5 - Detect & Report SNP genotypes, CNPs
- BiRW - Reconstruct Disease Phenome-genome Association
- Bis-SNP 0.82.2 - Bisulfite Space Genotyper & Methylation Caller
- BLink 3.0 - compute Linkage Disequilibrium based on a Bayesian estimate of D'
- BLR 1.6 / BGLR 1.0.8 - Bayesian Linear Regression
- BLUP_GEN / BLUP_SNP - Estimate Solutions for Genomic Selection Models
- BMapBuilder 3.1 - Build Chromosome-wide LD Maps
- bnpsd 1.2.3 - Model and Simulate Admixed Populations
- BOG 2.0 - Identifying differentially Regulated Genes in the light of Gene Functions
- BoNB 1.2 - Biomarker Selection and Classification from Genome-wide SNP data
- BOOGIE - Predicting Blood Groups from High Throughput Sequencing Data
- BOOST 20101230 / GBOOST 20130821 - Detect Gene-gene Interactions
- Bootstrapper 1.0 - Haploblock Border Reliability Estimation tool
- BOTTLENECK 1.2.02 - Detect Recent Effective Population Size Reductions from Allele Data Frequencies
- BottleSim 2.6.1 - Population Bottleneck Simulator
- BPPH - Perfect Phylogeny Haplotyper
- BPrimm 1.12 - Bayesian and Penalized Regression in Multiple Loci Mapping
- BQTL 1.0-33 - Map Genetic Traits
- BR_squared 1.12 - Bias-Reduced estimates via Bootstrap Resampling Association
- BreakFusion 1.0.1 - Identify Gene Fusions from paired-end RNA-Seq data
- BreakPtr 1.0.5 - Discovery of unbalanced Structural Variants with Tiling Microarrays
- BreakTrans 0.0.6 - Uncover the Genomic Architecture of Gene Fusions
- Breeder 3.0 - Plant Breeding Game
- Broad-Enrich 2.14.0 - Gene Set Enrichment Testing for Sets of Broad Genomic Regions
- BUS 1.48.0 - Gene Network Reconstruction
- CADD 1.6 - Estimating the Relative Pathogenicity of human Genetic Variants
- CAGExploreR 1.0.2 - Analysis and Visualization of Promoter Dynamics across multiple experiments
- CalcMatch 1.12 - Concordance between two sets of Genotype data
- CAMBa - Coverage Aware Mutation calling using Bayesian analysis
- CAMer - R package for Continuous Admixture Modeling
- CAMP - Coalescent based Association Mapping
- CancerMutationAnalysis 3.0 - R Software for Cancer Mutation Analysis
- CancerMutationMCMC 0.1-1 - Estimate Somatic Mutation Rates
- CandiSNP 0.3.1 - Identifying Candidate SNPs in Genomes
- CanSNPer 1.0.10 - A Hierarchical Genotype Classifier of Clonal Pathogens
- caOmicsV 1.20.0 - Visualization of Multi-dimentional Cancer Genomics data
- CAPL 4.1.8 - Combined Association in the Presence of Linkage
- CAROL - Combined Functional Annotation Score Tool
- CARROT - ClAssification of Relationships with ROTations
- CASPAR - Conditional Linkage Analyses
- CatchAll 4.0 - Estimating the Number of Species
- CaTS 0.0.2 - Power Calculator for Two Stage Association Studies
- CAVIAR - CAusal Variants Idenfitication in Associated Regions
- CC-QLS 1.3 - Case-Control Quasi-Likelihood Score test
- CCAT - Combinatorial Code Analysis Tool for Transcriptional Regulation
- CCH 20141012 - Identify Genomic Regions of Shared Ancestry
- CCRaVAT / QuTie - Rare Variant Analysis software
- ccSVM - Correcting Support Vector Machines for Confounding Factors in Biological data Classification
- CDAO 2019-06-26 - Comparative Data Analysis Ontology
- CDFISH 0.55 - Landscape Genetics program to Simulate Gene Flow
- CDPOP 1.2.32 - Spatially-explicit Cost Distance Population Genetics program
- CDS-plotcon - Detect Enhanced Conservation in Coding Sequences
- Celestial3D 1.0.1 - Graphical Display of Familial Information
- CEPSKAT 1.0 - Continuous Extreme Phenotype SKAT
- CERVUS 3.0.7 - Parentage Analysis
- CES 1.0 - Codon Evolution Simulation
- CFC 1.0 - Monitor Genetic Diversity
- CGEN 3.28.0 - Genetic Analysis of Case-Control Data
- CGI - Prioritize Genes by Integrating Expression data and Protein Interaction data
- cgmisc 2.9.11 - Enhanced Genome-wide Association Analyses and Visualization
- CGR 1.0-5 - Classic Genetics in R
- changePedStrand - Change Strand for a Pedigree file
- Chaplin 1.2.3 - Case-control Haplotype Inference package
- CHASM 3.0 / CHASMplus 1.0 - Cancer-specific High-throughput Annotation of Somatic Mutations
- CHB 1.0 - Coalescence-guided Hierarchical Bayesian
- Chi8 v1 - GPU program for Detecting Significant Interacting SNPs with the Chi-square 8-df test
- CHIAMO 0.2.1 - Genotype Calling Algorithm for Multi-cohort Study
- Chimera - Exploiting Hidden Information Interleaved in the Redundancy of the Genetic Code
- CHIP2SPELL 1.0.2 - Generate Input files for Alohomora_m
- ChromatoGate 1.2 - Analyze / Edit Chromatogram data
- CHROMIBD 1.1 - Estimation of Identity-by-Descent Probabilities between Haplotypes and Genotyped Ancestors
- ChroMoS - SNP Classification, Prioritization and Functional Interpretation
- CHuM - Cis-acting Human Mutation
- CisEvolver - Molecular Evolution Simulation Program
- CisModule 20051205 - De novo Discovery of Cis-regulatory Modules
- CITE 1.0 - Confidence Intervals for Divergence Time Estimates
- Clarki 20090715 - Use SNP data for Species Identification
- Clean_tree 2 - High-resolution Male Lineage Classification
- CLImAT 1.2.2 - Detection of Copy Number Alteration and Loss of Heterozygosity
- ClinLabGeneticist 2.28 - Diagnosis of Pathogenic Variants from WES data
- ClonalFrame 1.2 / ClonalFrameML 1.12 - Inference of Bacterial Microevolution using Multilocus Sequence data
- CloseUp - Detect Chromosomal Homology Using Gene Density Alone
- Clumpak 20150326 - Model-based Population Structure Analysis
- CLUMPHAP 1.1 - Haplotype-based Association Analysis
- CLUMPP 1.1.2 - Label Switching and Multimodality problems in Population-genetic Cluster Analyses
- CLUSTAG - Hierarchical Clustering and Graph Methods for Selecting Tag SNPs
- cM Converter - Convert in Batch Physical to Genetical Map Positions of Molecular Markers of Rice
- CMDS 1.0 - Identify Recurrent DNA Copy Number Changes
- CNALR 1.0 - Stratification of Tumour Subtypes based on Copy Number Alteration Profiles
- CNAmet 1.2.1 - Integrate Copy Number, Methylation and Expression data
- CNAseg 1.0 - Identify CNVs in cancer from NGS data
- CNGen 1.0.1 - Convert Integrated SNP and CNV Calls into Phased Copy Number Genotypes
- CNSuite - caBIG Analytical Tool for Copy Number analysis
- CNV Workshop 2.0.11 - Analyzing Genome Variation such as Copy Number Variation (CNV)
- CNVAnalyst - Statistical, Bioinformatic, and Visual Analyses of CNVs
- CNVannotator 20131114 - Annotation Server for Copy Number Variation (CNV) in Humans
- cnvCapSeq 0.1.2 - Detecting & Genotyping CNV in Long-range Targeted Resequencing
- cnvCSEM - CNV-guided Multi-read Allocation for ChIP-seq
- CNVDetector 1.1 - Locate Copy Number Variations using Array CGH data
- CNVEM 0.710 - Infer Carrier Status of CNVs in Large Samples from SNP Genotyping Data
- CNVer 0.8.1 - method for Detecting Copy Number Variation
- CNVfam - Detecting CNV in nuclear families Genotyped using the Illumina platform
- cnvHiTSeq 0.1.2 - Detect and Genotype CNVs in WGS data
- CNViewer 2.1 - Analysis and Comparison of Copy Number Variation (CNV)
- CNViewer 20111128 - Identification of Duplications, Insertions or LOH that Segregates with a Disease Phenotype
- CNVineta 1.0-1 - Data mining tool for large case-control copy number variation data sets
- CNVision 1.0 - Copy Number Variation Analysis software
- CNVnator 0.3 - CNV Discovery and Genotyping from Depth of Read Mapping
- cnvOffSeq 0.1.2 - Detecting & Genotyping intergenic CNVs using off-target Exome data
- CNVphaser / CNVphaserPro 1.1 - Infer CNV Haplotypes with Variations
- CNVstat 1.0 - Statistical Association Analysis of Copy Number Variants (CNVs)
- CNVtools 134.6 - Robust CNV Case Control and Quantitative Trait Association
- CoaCC 1.0.1 - Simulate Case-control Study using Coalescent Framework
- Coancestry 1.0.1.2 - Simulate, Estimate and Analyse Relatedness and Inbreeding Coefficients
- COB - Estimating Recombination Rates
- COCA - Knowledge-guided Gene Ranking
- COCO-CL - Identify Orthologous set of Genes.
- CODA 1.1 - Quantitative Characterization of Crossover Position Patterns along Chromosomes
- CodABC 2.0.0b - Coestimation of Recombination, Substitution and Molecular Adaptation Rates by Approximate Bayesian Computation
- COE 0.0.5 - Genome-Wide Two-Locus Epistasis Test in Disease Association Study
- Coevol 1.5 - Correlated Evolution of Substitution Rates and Phenotypes
- CoGAPS 3.10.0 - Coordinated Gene Activity in Pattern Sets
- CollapsABEL 0.10.11 - Generalized CDH (GCDH) Analysis
- coloc 5.1.0 - Colocalisation Tests of Two Genetic Traits
- COLONISE 1.0 - Study Colonization Processes in Metapopulations
- COLONY 2.0.6.7 - Parentage and Sibship Inference from Multilocus Genotype data
- COMBASSOC 1.3 - Overall Significance of Multiple analysis
- Combined_LRT 1.0 - Combined Likelihood Ratio Test for Candidate Gene Studies
- Concatenate Haplotypes 0.03 - Concatenate Two Sets of Haplotypes
- CoNCoS 0.2 - Copy Number Estimation with Controlled Support
- CoNe 1.01 - Estimate Ne from two temporal samples
- CONEXIC - COpy Number and EXpression In Cancer
- ConSAT 1.1 - Annotation of Gene Families
- conStruct v1.0.3 - Modeling Continuous and Discrete Population Genetic Structure
- Control-FREEC v11.6 - Control-free CNVs Detection using Deep-sequencing data
- Convergence - Calculate Divergence and Convergence using Modifications of the Codeml program
- Copy Number Explorer 1.3 - Interactive Copy Number Analysis for Cancer Genomics
- CopyMap 0.813 - Localization of Copy Number Variation
- CoVaMa 0.7 - Co-Variation Mapper for Disequilibrium Analysis of Mutant Loci
- CovIBD - Linkage Analysis of Affected Sibpairs
- CPAG 0.2 - Cross-Phenotype Analysis of GWAS
- CPCrand beta - Randomization Test of the Common Principal Component Model
- CPSIM - Genetic Maps & Markers Simulation
- Crann 1.04 - Detect Adaptive Evolution in Protein-coding DNA Sequences
- CRaVe 0.0.2 - Association Tests between sets of SNPs and a Phenotype
- Cri-Map 2.4 - Construct Multilocus Linkage Map
- CrypticIBDcheck 0.3-3 - Identifying Cryptic Relatedness in Genetic Association Studies
- CSI - Construct Confidence set of Markers within prespecified Genetic Distance from the Disease Locus
- CSim 20000614 - Simulation program for Somatic Cancer Evolution
- CSMinFinder - Chromatin State with Minimum length Finder
- CSSL Finder 0.9b1 - Develop Chromosome Segment Substitution Lines
- CSTP 1.0 - Condition-specific Target Prediction from Motifs and Expression
- CubeX - Calculation of Pairwise Linkage Disequilibrium using Exact Solution
- CVhaplot 2.01 - Consensus tool for Statistical Haplotyping
- CYNTENATOR 20101005 - Progressive Gene Order Alignment of 17 Vertebrate Genomes
- Cypiripi - Exact Genotyping of CYP2D6 using High-throughput Sequencing data
- Cyrillic 3.0.400 - Pedigree Drawing program designed for Clinical Geneticists
- D-GEX 1.01 - Deep Learning for Gene Expression Inference
- DaDi 1.6.3 - Fit Population Genetic Models using a Diffusion Approximation to the Joint Frequency Spectrum
- DAFGA 1.0 - Diversity Analysis of Functional Gene Amplicons
- DANN - Annotating Pathogenicity of Genetic Variants
- DAPPLE v0.17 - Disease Association Protein-Protein Link Evaluator
- DASH 1.1.0 - DASH Associates Shared Haplotypes
- DawnRank 1.2 - Discovering Personalized Driver Mutations in Cancer
- DBGSA 1.2 - Distance-based Gene Set Functional Enrichment Analysis
- DBM - Dynamic Bayesian Markov model for Genotype Calling
- DeAnnCNV - Detection and Annotation of Copy Number Variations from Whole-exome Sequencing data
- DEEGEP - Density Estimates by Expansions of GEgenbauer Polynomials
- DeepGS 1.2 - Predicting Phenotypes from Genotypes using Deep Learning
- deepSNV 1.32.0 - Calling Subclonal SNVs from paired Deep Sequencing Experiments
- DELISHUS - Computing Genomic Deletion Variation
- DemoDivMS 0.2 - Predict Genetic Diversity at Microsatellite DNA Marker
- DendroUPGMA 201410 - A Dendrogram Construction Utility
- DeNovoGear 1.1.1 - Detect denovo Mutations using Sequencing data of Related Individuals
- DESnowball 1.0 - Method to Identify Downstream Target Genes that are affected by a recurrent driver Mutation
- detect-NAHR - Identifying Non-allelic Homologous Recombinations
- DetSel 1.0.3 - Detect Markers Responding to Selection
- DetSex 1.0 - Assigning Marker to their Chromosome Type and Sexing Individuals from Genotyping data
- DHLAS - Web-based Information System for Statistical Genetic Analysis of HLA Population data
- DHSMAP 2.0 / DHS-R - Fine-mapping of Qualitative Traits by use of Linkage Disequilibrium
- Digital Karyotyping 1.0.1 - Detecting DNA Copy Amplifications
- DILTAG - Inferring the Evolutionary History of Gene Clusters from Phylogenetic and Gene Order Data
- DiNAMIC - Identify recurrent DNA copy number Aberrations in Tumors
- DiNuP 1.3 - Identify Regions of Differential Nucleosome Positioning
- DiRE - Identification of DIstant Regulatory Elements of co-regulated Cenes
- discoSnp 2.5.4 - Discovering SNPs without requiring any reference Genome
- discovering-cse 0.32 - Discovering Context-Specific Sequencing Errors
- disentangler 20111001 - Linkage Disequilibrium Mapping and Haplotype Analysis
- diSNPselection - Disease Informative SNP Selection for Gene-based Association tests
- DISSCO 1.0 - Direct Imputation of Summary Statistics allowing COvariates
- DIST 1.0.0 / DISTMIX v0.2.0- Direct Imputation of summary STatistics for unmeasured SNPs /from mixed Ethnicity Cohorts
- DISTANCE - Plot Genetic Distances between Populations
- DistMiss 1.0 - Compute Matrix of Genetic Distances between Populations
- DistPCoA - Principal Coordinate Analysis with Correction for Negative Eigenvalues
- distruct 1.1 - Graphical Display of Population Structure
- DIVERGE 2.0 - Detect Functional Divergence between member Genes of a Protein Family
- DIYABC 2.1.0 - Approximate Bayesian Computation for Inference on Population history
- DLMM 0.0.2 - Double-layered Mixture Model for Joint Analysis of Copy Number and Gene Expression Data
- dmGWAS 3.0 - Genome-wide Association Studies (GWAS) Analysis
- DMLE 2.3 - Disease Mapping using Linkage disEquilibrium
- DNAMIX 3.2 - Calculate Likelihood Ratios for Mixed DNA Samples Encountered in Forensic Science
- DNC-MIX - Model Distribution of Gene Expression Profile of Test Sample as Mixture of Distributions
- DNENRICH - A framework for Calculating Recurrence and Gene-set Enrichment for de novo Mutations
- DominantMapper 20110207 - Analysis of SNP data for rapid Mapping of Dominant Diseases in related Nuclear Families
- DoRIS 0.1 - Demographic Inference based on shared IBD Haplotypes
- dose2geno - Generate Best Guess Genotypes from Dosage and Info File
- doseR2 - Dosage r2 Calculator
- DPPH - Perfect Phylogeny Haplotyping
- DPSAT 2.2 - DNA-Protein Sequence Analysis Tool for Android
- drawGenealogy 1.1 - Interactive Drawing of Family Histories
- drawWrightFisher 1.0 - Interactive Drawing of Lines of Descent under the Wright-Fisher Model of Evolution
- DRBTool - Determine HLA Genotypes at the DRB1 locus
- Drifter - Simulates Allele Frequencies using Forward-in-time Evolution under the Wright-Fisher model
- DRIVeR - Diversity Resulting from In Vitro Recombination
- DSS - Haplotype Inference for Large Families
- DTECD - Decision Tree Ensembles for InteraCtion Detections
- DualBrothers 1.1 - Recombination Detection Software
- DupHMM - Detect Copy Number Variants from SAM files
- easyGWAS - Platform for performing Genome-wide Association Studies
- easyLINKAGE 5.08 - Graphical User Interface for Automated Linkage Analyses
- EASYPAT 8.3 - Calculation of Likelihood Ratios for Single Locus data
- EasyQC 23.8 - Quality Control of Genome-wide Association Meta-analyses
- EasyStrata 8.6 - Evaluation of Stratified Genome-wide Association Meta-analysis data
- ebGenotyping 2.0.1 - Genotyping and SNP Detection using Next Generation Sequencing Data
- eBURST v3 - Displaying the Relatedness among Isolates of Bacterial Species
- ECLIPSE 1.1 - Error Correcting Likelihoods In Pedigree Structure Estimation
- EcMap - Evaluate the size of Families for Linkage analysis
- Eco-Gene 1.0 - Combine Population Genetic and Population dynamic processes with Forest Growth Models
- EDEN - Evolutionary Dynamics within Environments
- EditGDS 1.0 - A visual tool for Browsing and Editing GDS files
- EffiSim - Measuring Efficiency of Mutations Screens for Recessive Phenotypes
- EggLib 3.0.0 - C++/Python library and program package for Evolutionary Genetics and Genomics
- EH 24 - Estimate Linkage Disequilibrium between Different Markers
- EH+ / EHPLUS 2.0 - Model-free Analysis and Permutation tests for Allelic Association
- eHAP 2.0 - Analyze Multilocus data as Haplotypes
- EigenCorr 0.2 - Control of Population Stratification by Correlation-selected Principal Components
- EIGENSOFT 7.2.1 - Population Structure , Eigenanalysis & Stratification
- EIGENSOFT plus 1.0 - Principal Components Analysis for Performing GWAS QC and primary analysis.
- EINVis 20121021 - A Visualization tool for Analyzing and Exploring Genetic Interactions in Large-scale Association Studies
- Eip 1.0 - Epistatic Interaction Package
- ELA - Genetic Association Mapping method for Complex Diseases
- ELAI - Efficient Local Ancestry Inference
- eLSA 1.0.2 - Finding Time-Dependent Associations in Time Series Datasets
- EM - Estimate Genetic Distances and Chiasma Distribution for Human UPD and Trisomy data
- EM-NM - Network Motif Identification in Stochastic Networks
- EM-SNP - Allele Frequency Estimation, SNP Detection and Association Studies
- EMCmodule 0.1 - Discovery of Transcription Regulatory Modules using Evolutionary Monte Carlo
- EMINIM 1.01 - Expectation-Maximized INtegreative IMputation
- EMK 1.0 - Extended Monks and Kaplan
- EMLRT 1.0 - Expectation-Maximization Likelihood Ratio Tests for Post-Imputation Association Analysis
- EMMA 1.1.2 - Efficient Mixed-Model Association
- EMMAX Beta - Efficient Mixed-Model Association eXpedited
- Encore 1.1 - GWAS and Biological Data Analysis tool
- Endeavour 3.71 - Prioritization of Candidates Genes
- Endog 4.8 - Analyse Pedigree Information
- Enrichr - HTML5 Gene List Enrichment Analysis Tool
- ENT 1.0.2 - Genotype Phasing by Entropy Minimization
- Entropy - Uses an EM algorithm for Haplotype Frequency Estimation
- EPDT 1.0 - Extended Pedigree Disequilibrium Test
- EPIBLASTER 1.0 - Two-locus Epistasis Detection Strategy using GPU
- EPIGPUHSIC 1.0 - Compute HSIC between all possible interaction of SNPs and a Quantitative Phenotype
- EPIQ beta - Efficient Detection of SNP-SNP Epistatic Interactions for Quantitative Traits
- EPISNPmpi 4.2 / epiSNP 4.2 - Epistasis Testing in Genome-wide Association Studies
- EPISTACY 2.0 - Detect Two-locus Epistatic Interactions using Genetic Marker information
- Epistasis-HS - Assess the Degree of Epistasis for a given Trait
- Epiviz 3.0 / Epivizr 2.22.0 - Visualization Tool for Functional Genomics data
- EPSILON - eQTL Prioritization using Similarity Measures derived from Local Interaction Networks
- eQTLexplorer 6.0 - eQTL Visualization tool
- eQTNMiner 2.0.0 - High-resolution Mapping of Quantitative Trait Loci
- ERC - Evolutionary Rate Covariation Analysis
- ERCS 1.0.1 - Coalescent Simulations in Continuous Space
- eSNV-Detect v1.0 - Reliable Identification of Variants Using RNA-seq Data
- ET-TDT - Evolutionary Tree-Transmission Disequilibrium Test
- EvA 2.2.0 - Java based framework for Evolutionary Algorithms
- EVE - Evolution in Variable Environments
- Evian 2.1.0 - Evidential Analysis of Genetic Association Data
- Evoker 2.2 - Graphical Tool for Visualising Genotype Intensity data
- EvolSimulator 2.1.0 - Simulation Test Bed for Hypotheses of Genome Evolution
- EvolveAGene 4.02 - DNA Coding Sequence Evolution Simulation program
- ExomeCNVTest 0.51 - Identify Disease-associated CNVs
- ExomePicks 20100412 - Suggest Individuals to be Sequenced in a Large Pedigree
- ExonFinder 2.0 - Extract novel Cassette Exons/Retained-introns
- EXPANDS 2.1.2 - Expanding Ploidy and Allele-Frequency on Nested Subpopulations
- ExRAT - Tools for Association Study with Interaction
- eXtasy 0.1 - Variant Prioritization by Genomic data Fusion
- ExtractImputed 0.05 - Extract Information for a Subset of Sites from Imputed Dataset
- Ezimputer v3 - A workflow for Parallelized Genome Wide Imputation
- F-SKAT 2.0 - SKAT for Non-continuous Traits in Familial GWAS Data
- FAM-MDR - Family-Based Multifactor Dimensionality Reduction
- FamAgg 1.21.2 - Pedigree Analysis and Familial Aggregation
- FAMD 1.31 - Dominant Fingerprint Data Handling and Analysis
- Famdenovo 0.1.1 - Calculating the probability of being de novo for a Genetic Mutation using family history data
- FAMHAP 19 beta - Haplotype Association Analysis Software
- FamLBL 1.0 - Detecting Rare Haplotype Disease Association Based on Common SNPs Using Case-Parent Triads
- FaMoz 200906 - Software for Parentage Studies
- famRvTest 2.4 - Rare Variant Association analysis
- FamSeq 1.0.3 - Calculating Probability of Variants in Family-based Sequencing data
- famSKAT-RC 20140725 - Combining Family- and Population-based Imputation data for Association analysis of Rare and common Variants in large Pedigrees
- Famsphere 0.4 - Parental Allocation from known Genotypic Pools
- FAPI 0.1 - Fast and Accurate P-value Imputation for Genetic Association
- FAST 2.4 - Fast ASsociation Tests for Genes
- FaST-LMM 2.0.7 - FActored Spectrally Transformed Linear Mixed Models
- FastANOVA 0.0.5 - Perform ANOVA Tests on SNP-pairs in Batch mode
- FASTEH+ / FASTEHPLUS - Model-free Analysis and Permutation Test(s) of Allelic Association
- FastEPRR 2.0 - Fast Estimation of Population Recombination Rates
- FASTER 1.0 - Reduce Family Members for GENEHUNTER program
- fastlink 4.1P - Improved Version of LINKAGE
- FastMap 2.0 - Fast Association Mapping in Heterozygous Populations
- fastPHASE 1.4.0 - Haplotype Reconstruction & Estimating Missing Genotypes
- FastPop - Infer Intercontinental Ancestry using Genetic data
- FastQTL 2.184 - Fast and Efficient QTL mapper for thousands of Molecular Phenotypes
- FASTRUCT 1.01 - Analysis of Population Genetics and Individual Assignment
- fastsimcoal2 2.6.0.2 - Continuous-time Coalescent Simulator of Genomic Diversity
- FastSMC v1.1 - Estimate Pairwise identical-by-descent (IBD) Regions in Genome
- fastStructure 1.0 - Inferring Population Structure from SNP Genotype data
- FastTagger 1.0 - Genome-Wide Tag SNP selection
- Fatsim - Simulate the Effect of extracting/not extracting lipids on the outcome of stable Isotope Mixing Models
- FAVR 1.0 - Filtering and Annotation of Variants that are Rare
- FBAT v2.05_beta - Family-Based Association Test
- FEST 0.0.6 - Simulations and Likelihood Calculations of Pair-wise Family Relationships
- FESTA 2.0 - Fragmented Exhaustive Search for TAgSNPs
- FEstim 1.3.2 - Estimation of the Inbreeding Coefficient of Individuals
- FFPopSim 2.0 - Forward Simulation package for the Evolution of large Populations
- FGAP 060302 - Family Genotype Analysis Program
- fGWAS 2.0 - Functional GWAS software
- FILTUS 1.0.5 - Analysis of Exome Sequencing data
- FINDHAP V4 - Find Haplotypes and Impute Genotypes
- FINDSIRE - Identify Mothers or Sires
- FINEMAP 1.4 - Efficient Variable Selection using summary data from Genome-wide Association Studies
- fineSTRUCTURE 4.0.1 - Identify Population Structure using Dense Sequencing Data
- FISH 0.2 - Fast Genotype Imputation with Segmental Hidden Markov model.
- FishingCNV 2.1 - Detecting rare Copy Number Variations in Exome-sequencing data
- Fitchi - Haplotype Genealogy Graphs based on Fitch Distances
- fitTetra 1.0 - Genotype Calling of Tetraploid Samples based on bi-allelic Marker Assays
- Flapjack 1.22.04.21 - Graphical Genotype Visualization
- FLK - Detect Selection in Population Trees
- Flux Capacitor 1.6.1 - Quantify Expressed Sequence Features from Transcriptome
- FOG 1.0 - A tool to Map Genomic Features on to Genes
- forqs 2015 - Forward-in-time Simulation of Recombination, Quantitative traits, and Selection
- ForwSim - Population Genetic Simulators
- FPG - Forward Population Genetic Simulation program
- FRANz 2.0 - Reconstruction of Pedigrees
- frappe 1.1 - Estimating Individual Ancestry Proportion
- FreeNA 20091116 - Analysis of Microsatellite Dataset Harboring Null Alleles
- FREGENE - Aimulate Sequence-like data in large Genomic Regions and large Populations
- FSDA - Fragment Size Distribution Analysis for non-invasive prenatal CNV prediction
- FSuite 1.0.4 - Exploiting Inbreeding in dense SNP chip and Exome data
- FUEATEST - Fast Unbiased and Exact Allelic Test
- FUGUE 0.2.3 - Haplotype Frequency Estimation
- FunciSNP 1.32.0 - Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
- Funmap 2.2.1 - Functional Mapping Package for R
- fuzzyFDR 1.0 - Find Fuzzy Decision Rules for Multiple Testing of Hypotheses with Discrete data
- fwdpp 0.9.2 - C++ Template Library for Efficient Forward-Time Population Genetic Simulation
- G-to-A - Hypermutation Filter Generation using Expectation Maximization
- GADS 1.1 - Parametric Linkage Analysis of Quantitative Traits
- GAGA - Genetic Algorithm for Genetic Ancestry Method
- GAIN 0.2.0 - Genetic Association Interaction Network tool
- GAMETES 2.1 - Genetic Architecture Model Emulator for Testing and Evaluating Software
- GAP 2009 - Mining complex Cancer Genomic Profiles
- GAPIT v3- Genome Association and Prediction Integrated Tool
- GAS2 20061018 - Evaluating Statistical Significance in Two-Stage Genomewide Association Studies
- GASP 3.31 - Genometric Analysis Simulation Program
- GAssist - Genetic Classifier System
- GAT 1.3.4 - Genomic Association Tester
- GATOR 1.0 - Genetic Association Tests Based on Ranks
- GBIRP - Genotype-Based Identification of Relative Pairs
- gboosting 1.0.1 - High-dimensional Variable Selection
- GBSX 1.3 - Experimental Design and Demultiplexing Genotyping by Sequencing Experiments
- GC - Frequentist Genomic Control Software
- GControl - Bayesian Genomic Control Software
- GCORE 201510 - Fast Family-based Gene-gene Interaction Test
- GCPROG 2.6 - Association Analysis with Multiple Markers
- GCTA 1.01 - Genome-wide Complex Trait Analysis
- GCUA 1.2 - Evaluate Codon Usage in a set of Genes
- GDA 1.1 - Analyze Discrete Population Genetic Data
- GDL 1.1.0 - Genetic Data analysis Library
- gdsfmt 1.28.0 / SNPRelate 1.26.0 - CoreArray Genomic Data Structure (GDS) R Interface / Parallel Computing Toolset for GWAS
- GDT 0.1.1 - Genome-wide Association Analysis
- GEC 1.0 - Address Multiple-testing Issue with dependent SNPs
- GECOR - Power for Gene-Environment Interaction Tests in Matched Case-Control Association Studies
- GEDI 1.03 - Genotype Error Detection & Imputation
- GEDI-ADMX 1.03 – GEDI for Admixed Populations
- GEI-TRIMM - Gene-environment Interaction Triad Multi-marker Method
- GEmis - Power Calculations for Gene-Environment Tests Incorporating Misclassified Exposures
- GEMMA 0.94.1 - Genome-wide Efficient Mixed Model Association
- GeMS 1.0 - A High Efficient SNP Detection Software
- GemTools - Estimate Genetic Ancestry
- GenAlEx 6.51b2 - Population Genetic Analysis within Microsoft Excel
- GENBMAP 1.0 - Study of the Spatial Genetic Structure
- GenCo 200806 - Estimate Gene Conversion and Crossover Rates
- Gene characterization index - Assessing the Depth of Gene Annotation
- Gene Designer 2.0 - Design of Synthetic DNA Segments
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