Genetics & Pedigree
- PATHOGEN 1.11 – Study Adaptation in Structured Population in Microorganisms
- InVitroSimII – Simulate Barlow-Hall method of in vitro Evolution using StrataGene’s GeneMorph II kit
- Structure-Neighbor 2 – Estimate Relationships among Haploid Individuals
- EvolveAGene 3.06 – DNA Coding Sequence Evolution Simulation program
- MSTgold 2.2 – Calculates Minimum Spanning Trees
- EggLib 2.1.6 – C++/Python library and program package for Evolutionary Genetics and Genomics
- DECONSTRUCT – Pedigree Analysis
- POPSTAT – Determine Sample Sizes required to Reveal Population Structure
- CoalFace 0.3b – Simulation of the Coalescent Process with the visual display of Gene Genealogies
- CDPOP 1.2 – Spatially-explicit Cost Distance Population Genetics program
- CDFISH 0.51 – Landscape Genetics program to Simulate Gene Flow
- genePed 2.0 – Gene Genealogy Simulator based on Organismal Pedigree
- BottleSim 2.6 – Population Bottleneck Simulator
- BayeSSC – Bayesian Serial SimCoal
- PleioGRiP 0.02 – Genetic Risk Prediction with Pleiotropy
- Haplore 2.42 – Haplotype Reconstruction in pedigrees
- Dynamic-Trait – Nonparametric Autoregressive Model for Dynamic Trait Association Analysis
- StructHDP – Inference of number of Clusters and Population Structure from Admixed Genotype data.
- Structured Input-output Lasso – Leveraging input and output Structures for Joint Mapping of Epistatic and Marginal eQTLs
- Haploi – Haplotype Inference program for Multi-population data
- GFlasso – Association Analysis that Searches for Genetic Variation
- Spectrum – Joint Bayesian Inference of Population Structure and Recombination Events
- mStruct – Population Genetic Analysis of Microsatellite data
- GenAMap 3.1 – Visual Analytics Software Platform for eQTL and GWAS Analysis
- Tangram 0.2.2 – Structural Variation(SV) Detection based on MOSAIK Alignments
- Matrix eQTL 1.6.2 – Ultra fast eQTL Analysis via Large Matrix Operations
- BPrimm 1.12 – Bayesian and Penalized Regression in Multiple Loci Mapping
- asSeq 0.99.2 – Statistical Framework for eQTL Mapping using RNA-seq Data
- Sparse PCA – Sparse principal component analysis
- SMAT 0.98 – Scaled Multiple-phenotype Association Test
- CEPSKAT 1.0 – Continuous Extreme Phenotype SKAT
- MetaSKAT 0.27 – Meta-analysis for multiple markers
- SKAT 0.83 – SNP-set (Sequence) Kernel Association Test
- HAPPY – Haplotype Scoring for Generalized Linear Modeling and Haplotype-Disease Association Tests
- MULTIPOW 2.2 – Power for Multi-stage Genome-wide Association Studies
- GECOR – Power for Gene-Environment Interaction Tests in Matched Case-Control Association Studies
- PowerGxE – Power Calculations for Genetic Association Tests Exploiting Gene-environment Interaction
- GEmis – Power Calculations for Gene-Environment Tests Incorporating Misclassified Exposures
- CancerMutationAnalysis 2.0 – R Software for Cancer Mutation Analysis
- CancerMutationMCMC 0.1-1 – Estimate Somatic Mutation Rates
- OBO-Edit 2.3b5 – Ontology Editor for Biologists
- TransFIC – Transformed Functional Impact score for Cancer
- OncodriveCLUST 0.2 – Identify Genes whose Mutations are biased towards a large Spatial Clustering
- OncodriveCIS 1.1.0 – Assesses the Influence of Copy Number Alterations (CNA) in the Gene Expression
- OncodriveFM 0.0.1 – Uncover Driver Genes or Gene Modules
- Condel 20101221 – CONsensus DELeteriousness score of missense SNVs
- MAGMA 1.1 – Multiobjective Analyzer for Genetic Marker Acquisition
- Haploscribe 0.1.0 – Chromosomal Haplotypes by Genetic Phasing of Human Families
- ISCA 0.1.8 / ISCA plotter 120904 – Inheritance State Consistency Analysis
- Kaviar 20120425 – Queryable database of known Variants
- LDhat 2.2 – Analysis of Recombination Rates from Population Genetic Data
- CHAVA 1.0 – Estimate CNV Regions from CGH data using a HMM model
- AnA-FiTS 1.0.2 – Forward-in-time Simulator for Polymorphism data
- IBDmap – Identical by Descent Mapping
- Geppetto – Population Synthesis Software
- SNPsyn 1.1b – Gene Interaction Analytics Application
- SNP2GO 1.0 – Functional Analysis of Genome-Wide Association (GWA) studies
- MapInspect – Compare & Display Linkage Maps
- Peditree 2005 – Plant Pedigree Tree Drawing & Analysis
- GGT 2.0 – Visualization & Analysis of Molecular Marker Data
- CPSIM – Genetic Maps & Markers Simulation
- Pedimap 1.2 – Genetic & Phenotypic Data Visualization
- SMOOTH 7 – Clean of Data & Removal of Genotyping Errors
- Record 2.0 – Arranging Markers into Linear Order
- fitTetra 1.0 – Genotype Calling of Tetraploid Samples based on bi-allelic Marker Assays
- PedigreeSim – Simulation of Genotypes in Pedigrees of Diploid and Tetraploid Species
- Breeder 3.0 – Plant Breeding Game
- GIDetector – Detect Genomic Islands in Prokaryotic Genomes
- M3 20130108 – SNP Calling Algorithm for Illumina BeadArry Data
- QSAT – Quantitative Association Analysis
- Multiple TDT – Associate TDT type test for Nuclear-family data
- LORS – LOw-Rank Representation and Sparse Regression for eQTL mapping
- PSMix 1.1-2 – Population Structure Inference
- EM – Estimate Genetic Distances and Chiasma Distribution for Human UPD and Trisomy data
- markerSearchPower 1.0 – Calculate Statistical Power of Strategies Detecting Associated Markers
- Gene Locater – Genetic Linkage Analysis software using Three-point Testcross
- qps 1.0 – Simulate Populations evolving on a two-dimensional Continuum
- dmr 1.0 – Calculating the effect of Deterministic Neutral Evolution
- ERCS 1.0.1 – Coalescent Simulations in Continuous Space
- DBM – Dynamic Bayesian Markov model for Genotype Calling
- MosaicFinder – Identification of Fused Gene Families in Sequence Similarity Networks
- AbCD 20121004 – Arbitrary Coverage Design for Sequencing-based Studies
- MLNE 1.0 – Maximum-likelihood Estimate of Ne
- MER 3.0 – Estimate Pairwise Relatedness from Genetic Markers
- LEADMIX 1.0 – Likelihood Estimation of ADMIXture
- KinInfor v1 – Calculate Informativeness of Markers in Inferring Pairwise Relatedness
- COLONY 2.0.4.0 – Parentage and Sibship Inference from Multilocus Genotype data
- Coancestry 1.0.1.1 – Simulate, Estimate and Analyse Relatedness and Inbreeding Coefficients
- MEAdmix 1.0 – Molecular Estimator of Admixture
- MicroErrorAnalyzer 1.0 – Analyse Genotyping Errors of Microsatellites in Parentage Exclusion Analysis
- AgeStructure 1.0 – Estimate Effective Size & Generation Interval of Population with overlapping Generations
- PARENT-ASSIGN.XLS – Estimate minimal number of loci for Parentage Assignment
- POP-ASSIGN.XLS – Estimate minimal number of loci for Population Assignment
- PERM 1.0 – Detect Structuring Factors in meaningful Social Units
- PASOS 1.0 – Parental Allocation of Singles in Open Systems
- PAPA 2.0 – Package for the Analysis of Parental Allocation
- AFLPOP 1.1 – Population Assignment Program for AFLP data
- SOLOMON 1.0-1 – Parentage Analysis using Bayes’ Theorem
- NucleoFinder 1.0 – Detection of Nucleosome Positions
- MH-ESS 1.11 – Bayesian Analysis of Transposon Mutagenesis Data
- YGA – Identifying distinct Biological Features between Yeast Gene Sets
- HapMap filter 1.0 – Preprocess the HapMap Genotypic data for Association Studies
- Section 26 – Software Suite for Parsimonious Recombination Analysis of SNP data
- CarthaGene 1.3 beta – Genetic/Radiated Hybrid Mapping software
- GPSy – Gene Prioritization System for Conserved Biological Processes
- siliColony – Modifier Gene Analysis
- Overall LD – Assess the Overall Linkage Disequilibrium
- LDMgen – LD Mapping with Genotype Data
- LDMhap – LD Mapping with Haplotype Data
- FounderTracker – Genome-wide Detection of Founder Mutations in Cancer using Dense Tumor SNP Profiles
- LS-SNP/PDB – Genome-wide Annotation of Human SNPs
- CHASM 1.0.6 – Cancer-specific High-throughput Annotation of Somatic Mutations
- CRAVAT 1.0 – Cancer-related Analysis of Variants Toolkit
- HiDe 20120609 – Infer Highways of Horizontal Gene Transfer in the Evolutionary History of a set of Species
- PAIR 1.0 – Paired Allelic log-Intensity-Ratio-based Normalization method for SNP-CGH arrays
- EuGene 0.92 – Gene Optimisation Software
- MBMDR 3.0.3 – Model-Based Multifactor Dimensionality Reduction
- ANNOVAR 20130223 – functional ANNOtation of genetic VARiants
- Strelka 0.4.10.2 – Somatic Small-variant Calling from Sequenced Tumor-normal Sample Pairs
- CNV_SS – Copy Number Variation using Sacle Space
- mach2qtl 1.22 – Imputation-based Analysis of Quantitative Traits
- mach2dat 1.0.21 – Imputation-based Analysis of Binary Traits
- MaCH-Admix 2.0.198 – Genotype Imputation for Admixed Populations or with Large Reference Panels
- Heu-MCHC 1.0.2 – Heuristic Algorithm for the Haplotype Inference problem on Pedigree data with recombinations and mutations
- reHCstar 2.0.0 – Algorithm for Haplotype Inference problem on Pedigree data with Recombinations, Errors and Mutations
- GenABEL 1.7-4 – Genome-wide SNP Association Analysis
- Polymutt 0.13 – Calling Single Nucleotide Variants and Detecting de novo point Mutation
- Biofilter 2.0.0 rc 2 – Knowledge-driven Multi-SNP analysis of large scale SNP data
- analysis 0.8.3 – Evolutionary Genetic Analysis
- genomation 0.2.1 – R package for Graphics and Operations for Genomic
- gFeatMiner 1.5.0 – Analyze and Manipulate Genomic Data
- CNVer 0.8.1 – method for Detecting Copy Number Variation
- MedSavant – Search Engine for Genetic Variants
- GSMA 1.1 – Implementation of the Genome Search Meta-analysis Method
- REGENT 1.0.5 – Calculate Risks Conferred by Genetic Factors and Multi-level Environmental Factors
- GenoProof 2.2.7 – Kinship Cases and Population Studies
- PCAj – Population Structure Prediction System for Japanese
- Olorin 1.0.1 – Interactive Filtering tool for Next Generation Sequencing data
- Optimist 20120420 – Inference of Positive Selection
- optiCall 0.6.4 – Robust Genotype-calling Algorithm
- GFold 1.0.8 – Generalized fold change for Rank Differentially Expressed Genes from RNA-seq data
- IsoEM 1.1.1 – Inferring Alternative Splicing Isoform Frequencies from High-Throughput RNA-Seq Data
- treemix 1.11 – Inference of Population Trees with Admixture
- Stacks 0.99994 – Analyse RAD Sequencing data
- Migrate-N 3.4.4 – Estimate Population Sizes & Migration Rates
- GENOMEPOP 2.6.2 – Evolve Populations of Genomes under complex Evolution Models and Demography
- DistPCoA – Principal Coordinate Analysis with Correction for Negative Eigenvalues
- OmegaPlus 2.2.1 – Detection of Selective Wweeps in Whole-genome Datasets
- CohortComparator 1.3 – Identity Candidate Genes for Recessive Genotypes
- CNAmet 1.2 – Integrate Copy Number, Methylation and Expression data
- CANGES – Candidate Genes and SNPs
- SIMLD – Simulate Linkage Disequilibrium
- EMLD – EM Estimation of Haplotype Frequencies and LD calculation
- SNPTools 1.0 – SNP analysis in Next Generation Sequencing data
- BayesMendel 2.0-8 – R package for Mendelian Risk Prediction
- gdsfmt 0.9.11 / SNPRelate 0.9.9 – CoreArray Genomic Data Structure (GDS) R Interface / Parallel Computing Toolset for GWAS
- ALDER 1.02 – Compute Weighted Linkage Disequilibrium (LD) Curves
- HIBAG 0.9.4 – HLA Genotype Imputation with Attribute Bagging
- OptiMAS 1.4 – Decision Support tool to conduct Marker-Assisted Selection programs
- snpEff 3.1h / SnpSift 1.8 – Variant Annotation and Effect Prediction Tool
- Coevol 1.3 – Correlated Evolution of Substitution Rates and Phenotypes
- UTIL – Statistical Genetics UTILity programs
- SNPAssoc 1.8-5 – SNPs-based Whole Genome Association Studies
- SimPed – Generate Haplotype and Genotype data for Pedigree Structures
- OneMap 2.0-1 – Genetic Mapping in Outcrossing Species
- adegenet 1.3-6 – Exploratory Analysis of Genetic data
- VarSifter 1.5 – Analyse Sift Variation Data
- CaseControlIndGX 2 – Maximum-likelihood analysis of Case-control studies
- MultAssoc – Test of Association of a Disease with a Group of SNPs
- POPDIST 1.2.4 – Population Genetic data Analysis program
- Bagphenotype 0.22 – QTL mapping by bagging and subagging
- BayesDiallel 0.908 – MCMC Sampler for Analyzing Diallel Crosses of Inbred Strains
- Bagpipe 0.28 – Mapping QTLs in Populations descended from known founders
- PLAYPUS 0.2.0 – Integrated Variant Caller
- Genepop 4.2 – Population Genetics Software Package
- SNPWEIGHTS 1.0 – Inferring Genome-wide Genetic Ancestry using SNP Weights
- LTSOFT 1.3 – Analysis of Case-control Association Studies with known Risk Variants
- MIXSCORE 1.3 – Disease Scoring in Admixed Populations
- Illuminus – Genotype Calling algorithm
- Haplosuite 1.1 – R package for Haplotype Clustering and Visualization
- RegionalP 1.0 – Region-based meta-analysis of Genome-wide Association Studies in genetically Diverse Populations
- CSSL Finder 0.9b1 – Develop Chromosome Segment Substitution Lines
- MAPDISTO 1.76 – Map Genetic Markers in Experimental Segregating Populations Like Backcross
- MapChart 2.2 – Graphical Presentation of Linkage Maps and QTLs
- libsequence 1.7.5 – C++ Class Library for Population Genetics
- GEMMA 0.93 – Genome-wide Efficient Mixed Model Association
- varLD 1.0 – Comparison of Variation in Linkage Disequilibrium between Population
- HapFinder 1.0 – Finding common Haplotype Blocks in a database
- eCEO 0.11.01 – efficient Cloud Epistasis cOmputing model in Genome-wide association study
- FastTagger 1.0 – Genome-Wide Tag SNP selection
- CNVnator 0.2.7 – CNV Discovery and Genotyping from Depth of Read Mapping
- SVS 7.7 – Analytic Tools for Genomic and Phenotypic data
- SOLAR 6.6.2 – Genetic Variance Components Analysis
- GCTA 1.04 – Genome-wide Complex Trait Analysis
- IMPUTE 2.3.0 – Genotype Imputation in Genome-wide Association Study
- LOHAS 2.0 – Loss-of-heterozygosity Analysis Suite
- hwdglm 1.0 – Testing Hardy-Weinberg Disequilibrium Using Generalized Linear Model
- ARR 1.0 – Adaptive Ridge Regression for Rare Variant Detection
- Genome-wide Evaluation – Performs Genome-wide Evaluation
- PROC QTL 2.0 – SAS Procedure for Mapping Quantitative Trait Loci
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