2012 February
- AIRnet 0.9 – Infer Gene Regulatory Networks
- PSODA 0.96 – Phylogenetic Search tool
- GNUMAP 3.0.2 – Genomic Next-generation Universal MAPper
- DiANNA 1.1 – Cysteine state and Disulfide Bond partner prediction
- RNAmutants 1.1.0 – Exploring the Effects of Mutations on the Secondary Structure of RNAs
- RNApathfinder – Analyze Near-optimal Folding Pathways between RNA Secondary Structures
- RNA-WL – Thermodynamics of RNA structures by Wang-Landau sampling
- RNAborMEA – Maximum Expected Accurate Structural Neighbors of an RNA Secondary Structure
- VCAKE 2.0 – Genetic Sequence Assembler
- ConDens – Predict Kinase Substrates using Conservation of Local Motif Density
- RNAcontext – Predict the Sequence and Structure Preferences of RNA-binding proteins
- RankMotif++ – Motif Search
- FRESCO – Flexible Alignment with Rectangle Scoring Schemes
- VARiD 1.0.7f – Variation Detection
- RSEG 0.4.4 – Identify Epigenomic Domains from ChIP-Seq data
- RMAP 2.05 – Short-read Mapping
- DME 2 beta – Discover Transcription Factor Binding Site Motifs
- SHARCGS – SHort read Assembler based on Robust Contig extension for Genome Sequencing
- Batman 0.2.3 – Bayesian Tool for Methylation Analysis
- BAMseek 20110724 – Browse Large BAM and SAM Alignment Files
- Alta-Cyclic 0.2.2 – Base Caller for Illumina/Solexa Genome Analyzer
- GenGen 20100624 – Pathway-based Association Tests
- PennCNV 201106 – Copy Number Variation detection
- GEC 1.0 – Address Multiple-testing Issue with dependent SNPs
- IGG 3.0 – Integrate Genotypes for genome-wide Genetic studies
- PowerMarker 3.25 – Statistical Software for Genetic Marker data analysis
- DNAMIX 3.2 – Calculate Likelihood Ratios for Mixed DNA Samples Encountered in Forensic Science
- TAGster – Single or Multi-Population Tag SNPs Selection, Evaluation and Visualization
- PCR Analyzer v 1.02 – Estimate for Initial Amount of Amplicon Present in a PCR
- mPopTag – Multi-Population Tag SNP Picker
- EPIG – Extract Microarray Gene Expression Patterns and Identifying co-expressed Genes
- SVN – Remove Systematic Variation in Microarray Gene Expression data
- PAGE – Phase-shifted Analysis of Gene Expression
- Modk-Prototypes – Clusters Biological Samples
- ExP – Expression Predictor
- TRIMM – TRIad Multi-Marker
- GEI-TRIMM – Gene-environment Interaction Triad Multi-marker Method
- GAPWM 1.0 – Genetic Algorithm Method for Optimizing a Position Weight Matrix
- GADEM 1.3.1 – Motif Discovery tool for Large-scale Genomic Sequence data
- fdrMotif – Identify Cis-elements by an EM Algorithm Coupled with False Discovery Rate Control
- EpiCenter 1.7.0.8 – Analysis tool of Genome-wide mRNA-seq or ChIP-seq data
- HTR – Haplotype Trend Regression
- ELA – Genetic Association Mapping method for Complex Diseases
- HS-TDT – Haplotype Sharing Transmission Disequilibrium Test
- HomoVert 0.4.1 – Convert Entrez Gene IDs from one Species to another
- BACarray 0.6 – Analysis of BAC DNA arrays for Comparative Genomic Hybridization
- ArrayFun 1.0 – Analyze 2-color Expression Arrays
- pplacer 1.1 – Phylogenetic Placement and Subsequent Visualization
- ISM – One-Carbon and Glutathione Metabolism Modeling Software
- FSA 1.15.7 – Fast Statistical Alignment
- PIPS 1.0 – Phylogenetic Inference of Protein Stability
- TwoPhaseInd 1.0.0 – Two-Phase Independence
- SHARE 1.1.0 – Multi-locus Analysis
- powerGWASinteraction 1.0.0 – Power Calculations for Interactions for GWAS
- vBsr 0.0.1 – Fitting an Ultra-sparse Variational Bayes Spike Regression model
- ISS – In-silico Gene Sequencing Method
- MAGprediction – Gene Allele Prediction Using Unphased SNP data
- ProbePlus 1.0 – Analytic Tool for Analyzing Affymetrix GeneChip Gene Expression Array Data
- SignalViewer – Image Analysis of cDNA Microarrays
- PDPSys – Pedigree Data Processing System
- HPlus 4.0 – Haplotype Analysis
- METRADISC / METRADISC-XL – METa-analysis of Microarrays Datasets / Heterogeneity Testing
- DHLAS – Web-based Information System for Statistical Genetic Analysis of HLA Population data
- HEGESMA 2.0 – Genome Search Meta-analysis ang Heterogeneity testing
- HAPSIMU 1.0 – Genetic Simulation Platform based on real Haplotype Data
- SNPdetector 20051014- Sensitive and Accurate SNP Detection
- HapScope 20030203 – Analysis of Functionally Annotated Haplotypes
- EST_GENOME 5.2 – Align a Spliced DNA Sequence to an Unspliced Genomic Sequence
- ARIADNE 1.2 – Statistics of Sequence and Profile Alignments
- DSS – Haplotype Inference for Large Families
- HIT 1.0.1 – Haplotype Inference Technique
- HaploParser 0.1 – Haplotype Inference using Combinatoric Parsing
- BACH 1.1 – Fast Haplotype Inference via Context Tree Weighting
- MOODS 1.0.1 – MOtif Occurrence Detection Suite
- LASWG 0.5 – Local Alignment Statistics with Gaps
- HaploVisual 0.04 – Haplotype data Visualization and Analyzation
- HWSIM – Test Hardy Weinberg Ratios when Sample Sizes are small
- HAPLOT 3.2 – Graphical Presentation of Haplotype Block Structures
- AsVis 20051125 – Visualizing Association Rules in SNP Neighborhoods
- HPM / TreeDT – Association Analysis using Haplotype data or Genotype data
- HaploRec 2.3 – Haplotype Population-based Genotype data
- QAmerge 2.0 – Pool Replicated Microarray Datasets
- NGS-Motif-Power – Significance and Power of Pattern Occurrences in NGS reads
- RD – Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
- CEDER – Detection of Differentially Expressed Genes by combining significance of exons using RNA-Seq
- NePhe 1.0 – Network RNAi Phenotype Score
- Sub-GSE – Testing Gene Set Enrichment for Subset of Genes
- DynBin – Binning Microbial Community Profiles
- LocSim – Local Similarity Analysis for Microbial Community Profiles
- CGI – Prioritize Genes by Integrating Expression data and Protein Interaction data
- EM-NM – Network Motif Identification in Stochastic Networks
- Int-Path – Causal Gene Identification and Gene Regulatory Pathway Inference
- MitoDis – Detection of Mitochondrial DNA mutation Involvement in Diseases
- HapBlock 3.0 – Haplotype Block Partitioning
- GRAPPA 2.0 – Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms
- RNACluster 1.0 – RNA Secondary Structure Comparison and Clustering
- cBar 1.2 – Identification of Chromosomal Sequence Fragments from Metagenome data
- KOBAS 2.0 – Annotation and Identification of Enriched Pathways and Diseases
- SEAS 1.0 – System for SEED-based Pathway Enrichment Analysis
- GOST 0.1 – Detect Orthologous Relationship in Microbial Genomes
- QUBIC 1.0 – Biclustering Tool for Microarray Data
- PRIME 0.9 – Mass Spectrum Data Mining Tool
- PMAP II – Resolve pathway mapping problem with Operon and Regulon information
- JPOP 0.1 – Prediction of Operon Structures
- Cubic 2.0.4 / JCubic 1.1 – Protein Binding Site Prediction
- PROSPECT 2.0 – Threading-based Protein Structure Prediction System
- SpotLink 1.0 – Proteomics tool for Organization and Visualization
- Primegens 2.0.5 – Primer Design for Microarray
- PolyPhy – Microbial Phylogeny Reconstruction with Polytomy Identification
- Musite 1.0.1 – Prediction of Both General and Kinase-specific Protein Phosphorylation Sites
- MUPRED – Protein Secondary Structure Prediction
- GeneFAS – Gene Function Prediction
- DomainParser 2 – Protein Structure Domain Partition
- ComPhy – Genome Composite Distance Phylogeny for whole-genome phylogeney inferences
- CodonO – Analysis of Synonymous Codon Usage Bias
- CGHweb 1.0 – Analyze Array_CGH data with Multiple Algorithms
- QCC 1.1 – Measure Reproducibility of ChIP-chip data
- Repeat Enrichment Estimator – Measure Enrichment of Annotated Repeat Types in ChIP-seq data
- GoFish 1.11 – Find Genes with Combinations of Gene Ontology Attributes
- Synergizer – Provide Translations of Biological Database Identifiers
- ClusterJudge – Score the Results from any Clustering Algorithm
- ChIPper – Analysis of ChIP-chip data
- ARCT 0.9 – Comparative Genomics of Aging
- GEDI 2.1 – Analysis of Microarray Data
- AlignACE 3.0 – Motif Finding
- CurveSOM – Curve-based Custering of Time Course Expression data
- ILPMap 20110128 – Construct Consensus Genetic Maps under Comparative Analysis
- TAXFOLD – Improve Toxonomy-based Protein Fold Recognition
- KegArray 1.2.3 – Microarray Data Analysis & Cluster
- KegDraw 0.1.12 beta – Draw Compound & Glycan Structures
- med2bib 1.04 / toc2bib 1.04 – MEDLINE and TOC/DOC to BibTeX Conversion
- GenCompress 20080118 / GenDecompress – Compression / Decompression for DNA sequences
- LIden – Linkage Analysis Software
- NJtandem – Neighbor Joining Approach for Reconstructing Tandem Duplication History
- MRD – Finding Mutation Regions
- LDWP – Linked Region Detection without Pedigree
- MotifDetector – Finding Motifs in Multiple DNA sequences
- CTRD – Computing Translocation Distance between Genomes
- LocRepeat – Finding Regions of Pseudo-periodic Repeats
- ParaTree – Parametric Alignment of Trees
- ParaRNA 1.0 – Computing Parametric Alignment of Two RNA Structures
- mtree – Reticulate Networks of Multiple Phylogenetic Trees
- SEGID – Conserved Segment Identification
- HAPAR – Haplotype Inference by Parsimony
- Pedigree-Draw 6 – Genealogy Visualization
- PEDSYS 2.0 – Database System for Management of Genetic, Pedigree and Demographic data
- VEGAS 0.8.27 – Versatile Gene-based Association Study
- TWINSIM – Simulate Twin-nuclear Families in which QTLs and Linked Markers are Segregating
- Sib-pair 20111213 – Analyses of Family Data
- EIGENSOFT plus 1.0 – Principal Components Analysis for Performing GWAS QC and primary analysis.
- Annot 1.0 / PLINK2wakefieldBF 1.0 – Calculate Bayes Factors
- GenoQuickSim 20100309 – Simulates Genotypic data using Coalescent Methods
- GeneticDistances 20090824 – Calculate common Genetic Distances for Allele Frequency data
- Clarki 20090715 – Use SNP data for Species Identification
- SequenceViewer 20100606 – Viewing and Comparing DNA Sequences
- Mykiss 20100426 – Estimates Reproductive Success and Parentage using Genetic Data.
- StreamTree 20090303 – Map Genetic Differences between Populations
- GenotypeViewer 20070601 – Depicts Summary Statistics for a GENEPOP file
- HW-QuickCheck 20061121 – Check Genotypes for Agreement with Hardy-Weinberg Expectations.
- MM-Dist 20070306 – Estimating the Distribution of Genotypic Differences (mismatches) between Individuals in a Population
- ML-Relate 20080422 – Estimating Relatedness or Relationship from Genetic data
- ML-NullFreq 200906 – Estimates the Frequency of Null Alleles at Microsatellite Loci
- HP-Rare 20090202 – Rarefaction of Private Alleles and Hierarchical Sampling Designs
- ONCOR 20080424 – Genetic Stock Identification
- HYDEN – A software for Designing Degenerate Primers
- SIMBA – Organization of the Yeast Molecular Network by Integrated Analysis of Genome-wide Data
- CAMP – Coalescent based Association Mapping
- PSAT – Population Stratification Association Test
- RAT – A software for Rapid Association Tests
- ModEnt – Reconstructing Gene Regulatory Networks
- MetaReg – Graphical Interface for Modeling and Evaluation of Biological Systems
- MATISSE 1.1 – Detection of Functional Modules using Interaction Networks and Expression data
- Allegro 1.0 / Amadeus 1.2 – Motif Discovery Platform
- DASH 1.1.0 – DASH Associates Shared Haplotypes
- SXTestPlate 1.0.0 – Analyses Genotypes of a SNPlex™ Control Plate
- SNPSplicer 1.0.0 – Analyse SNP-dependent Splicing in Genotyped cDNAs
- SGCaller – Call Genotypes in Sequencing Traces
- Phobos 3.3.12 – Tandem Repeat search tool for Complete Genomes
- POPSIM 2.13 – Population Simulation program
- MFG Tools – includes GenoTool, PatientTool and SampleTool
- LIMS Tools – includes AssayManager, OrderTool and ProjectManager
- InSNP 1.0 – Detect Substitution and Indel SNPs in Sequencing Traces
- GMFilter 1.0.0 – Improves GeneMapper Analysis by removing bad wells
- Entropy – Uses an EM algorithm for Haplotype Frequency Estimation
- DRBTool – Determine HLA Genotypes at the DRB1 locus
- CNVineta 1.0-1 – Data mining tool for large case-control copy number variation data sets
- Genomizer 1.2.0 – Analysis of Genome Wide Association Experiments
- GIST 0.3 – Detect Association between Marker Genotypes and IBD sharing at the same locus
- PowerTrim – Preprocessing Family-Based Genetic Data
- PLATO 1.1 – Analysis of Genome-wide Association data
- LD-Plus – Display of Single SNP Statistics in the Context of Linkage Disequilibrium and Haplotype Structures
- PCAtag 2.1 – Selecte Tagging-SNPs using Principal Component Analysis
- TDT Power Calculator 1.2.1 – Power Calculation for the TDT
- GHOST 0.2.4 – Family-based Imputation and Association analysis
- GDT 0.1.1 – Genome-wide Association Analysis
- KING 1.4 – Identify Family and Population Structure
- GeneFinder 1.2.7 – Linkage Analysis with a Variety of Extensions
- BBSeq 1.0 – Analysis of RNA Sequence Count Data
- DWD – Perform Systematic Bias Adjustment in microarray data.
- FDM 1.0 – Analyze Differential Transcription
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