2012 January
- BigFoot – Bayesian Alignment and Phylogenetic Footprinting with MCMC
- SEQIO 1.2.2 – Read and Write Biological Sequence Files
- Strmat – String Matching and Pattern Discovery
- XPARAL 2.0a – Parameterized Alignment of Two Sequences
- DPPH – Perfect Phylogeny Haplotyping
- GPPH – Perfect Phylogeny Haplotyping
- LPPH – Perfect Phylogeny Haplotyping
- BPPH – Perfect Phylogeny Haplotyper
- COB – Estimating Recombination Rates
- Wright_Fisher_MP / Moran_MP – Multi-locus Match Probability
- Overpaint 0.2 – Joint Estimation of Gene Conversion Rates and Mean Conversion Tract Lengths from Population SNP data
- ASF – Two-Locus Asymptotic Sampling Formula
- HapBound-GC and SHRUB-GC – Detect Crossover and Gene-Conversion Recombinations
- HapBound / SHRUB – Detecting Crossover Recombination
- TMARG 1.0 – Association Mapping tool for Identifying Disease Associated Sites
- RecBlock – Find Optimal Mosaic Pattern for Recombinant Population SNP Sequences
- REAPER 1.0 – TagSNP Selection
- Bootstrapper 1.0 – Haploblock Border Reliability Estimation tool
- FastaGrep 2.0 – Search Oligonucleotide Binding Sites from FastA Genomic Sequences
- Peptidequant – Optimization-based Peptide Quantification tool
- SNPRuler – Predictive Rule Inference for Epistatic Interaction Detection in Genome-wide Association studies
- SNPHarvester – Detect Epistatic Interactions in Genome-wide Association studies
- MegaSNPHunter – Detect Disease Predisposition SNPs and High Level Interactions
- BOOST 20101230 / GBOOST 20110321 – Detect Gene-gene Interactions
- Genetranassoc 1.0 – Compute Association between Genome Loci and Expression Genetic Data
- TDTP 2.0 / TDT2G 2.0 – Software Implementing Multimarker TDTP / TDT2G
- rTDT 1.0 – software for TDT with missing data
- BiolAD-DB 3.0.1 – Informatics System for Clinical and Genetic Data
- FLOSS 1.4.1 – Ordered Subset linkage Analysis
- PRESTO 1.01 – Calculation of Order Statistic Distributions and Multiple-testing Adjusted P-values via Permutation
- BEAGLECALL 1.0.1 – Genotype Calling using Linkage Disequilibrium for unrelated individuals
- BEAGLE Utilities – Utility programs for Manipulating Large Data Files
- BEAGLE 3.3.2 – Genetic Analysis Software Package
- BAYESFST – Bayesian Estimation of Coancestry Coefficient FST
- API-CALC 1.0 – Calculate PIave for F-IS and F-ST
- H-Clust – Tag SNP Selection
- GControl – Bayesian Genomic Control Software
- GC – Frequentist Genomic Control Software
- ET-TDT – Evolutionary Tree-Transmission Disequilibrium Test
- tmax – Single Locus Tests for Association
- eHAP 2.0 – Analyze Multilocus data as Haplotypes
- PCHAT 2.2 – Principal Component of Heritability Association Test
- MHC v2 – Excess Allele Matching/Sharing in Extended Pedigrees
- Screen & Clean – Software for Identifying Genome-Wide Associations
- allelefreq – Bayes Allele Frequency Software
- CovIBD – Linkage Analysis of Affected Sibpairs
- Grouped FDR – Grouped False Discovery Rate
- GemTools – Estimate Genetic Ancestry
- weighted_FDR 1.2 – Apply Weighted False Discovery Rate for Multiple Testing
- BARS – Bayesian Adaptive Regression Splines
- BAMA – Bayesian Analysis of Multilocus Association
- ASPEX 2.5 – Affected Sib-pair Exclusion Mapping
- PATERN – Calculation of Paternity Probabilities
- FINDSIRE – Identify Mothers or Sires
- MUTPROF 0.2 / MUTCOMP 0.1 – Comparison of Mutation Profiles
- EASYPAT 8.3 – Calculation of Likelihood Ratios for Single Locus data
- ASP / ASPHARE – Calculator for Gene Mapping using a Sibpair Design
- TREAT 1.0.1 – Targeted RE-sequencing Annotation Tool
- SNPPicker 2 – tag SNP Selection Across Multiple Populations
- hweStrata 1.0 – Exact Stratified Test for Hardy-Weinberg Equilibrium
- Haplo Stats 1.5.2 – Statistical Methods for Haplotypes When Linkage Phase is Ambiguous
- bilinear.fit 0.1 – Preform Bilinear Regression Fits to 16O/18O Isotope Labeling
- Armitage 0.02 – Armitage Trend Chi-square Statistics
- fastlink 4.1P – Improved Version of LINKAGE
- SLINK 3.00 – Simulation program for Linkage Analysis
- Pedcheck 1.00 – Detecting Marker Typing Incompatibilities in Pedigree Data
- SNPCaller – Smarter Clustering Methods for SNP Genotype Calling
- QTL-ALL 1.0.1 – QTL Analysis and Linkage Library
- GMI 1.2 – Genetic Map Interpolator
- Mega2 4.5.4 – Manipulation Environment for Genetic Analyses
- SHAPE 1.3 – Biological Shape Analysis with Elliptic Fourier Sescriptors
- AntMap 1.2 – Software for Constructing Genetic Linkage Maps
- TIGER 1.02 – Identify Rapidly-evolving Characters in Evolutionary Data
- GCUA 1.2 – Evaluate Codon Usage in a set of Genes
- Crann 1.04 – Detect Adaptive Evolution in Protein-coding DNA Sequences
- EIGENSOFT 4.2 – Population Structure , Eigenanalysis & Stratification
- AUTOSCAN 1.0.3 – Easy Genome-wide Scans with Analyze
- CCRaVAT / QuTie – Rare Variant Analysis software
- GGSD 2.19 – Generic Genetic Studies Database
- CAROL – Combined Functional Annotation Score Tool
- ARIEL – Explore Effects of Rare Variants
- AMELIA – Allele Matching Empirical Locus-specific Integrated Association test
- HaploPainter 1.043 – Pedigree and Haploytype Drawing Tool
- Alohomora 0.33 – Linkage Analysis tools and Affymetrix Mapping
- ALLEGRO 2.0F – Linkage Analysis Package
- GFMCMC 1.0 – C Library of GLUT for Markov Chain Monte Carlo
- ChromoSeg 1.0 – Simulate and plot Ancestral Recombination Graphs
- NewHybrids 1.1 Beta3 – Gibbs Sampler Estimation of Hybrid Categories
- MCLEEPS 1.1 – Monte Carlo Likelihood Estimation of Effective Population Size
- Pedfiddler 0.6 – Manipulate Pedigree Graphs
- Loki 2.4.5 – Monte Carlo analysis of multiple QTL
- ECLIPSE 1.1 – Error Correcting Likelihoods In Pedigree Structure Estimation
- ALBERT – A Likelihood-Based Estimation of Risk in Trios
- HAPMIXMAP 1.0 – Model HapMap Haplotypes
- OMSSA 2.1.9 – MS/MS Peptide Spectra Identification
- STOCKS 2.0 – STOChastic Kinetic Simulation of Biochemical Processes
- runSBML 1.11 – Pathway Simulation Tool
- PNK 2e – Modeling and Simulation of Biological Processes
- Kinsolver – Simulator for Biochemical and Gene Regulatory Networks
- JigCell 7.1.0 – Modeling and Simulation software
- Metastats – Detect Differentially Abundant Features in Metagenomic Data
- MetaPath 0.83 – Comparative Analysis of Metabolic Pathways in Metagenomics
- RepeatFinder – Finding Repetitive Sequences Complete and Draft Genomes
- OperonDB 2.1 – Database of Predicted operons in Microbial Genomes
- TransTermHP 2.09 – Transcription Terminator Predictions
- Insignia 1.2 – Find Unique DNA Sequence
- sim4cc 20101122 – Cross-Species Spliced Alignment
- Celera Assembler 7.0 – Whole Genome Shotgun Assembler
- ELPH 1.0.1 – Estimated Locations of Pattern Hits
- ParaCountStudio 3.1.0 – Count Cell Numbers within Image
- SRTOOLS – Python Library for Short Read Analysis.
- MUNGO 1.0 – Python Library of Sequence Analysis
- Marcoil 1.2 – HMM-based Coiled-coil Prediction program
- Mapwhere 1.0 – Finds Perfect or Partial Matches to Motifs
- EffiSim – Measuring Efficiency of Mutations Screens for Recessive Phenotypes
- GBIRP – Genotype-Based Identification of Relative Pairs
- Haploclusters – Detect Excess Haplotypes Sharing
- Linkprep 2.9 – Create LINKAGE style files from AGRF style data
- Phat 20001215 – Find Genes in Eukaryotic Organisms
- CRITICA 1.05 – Microbial Gene Finder
- Glimmer 3.02 / GlimmerM 2.5.0 – Microbial Gene-finding System
- Bhageerath 1.0 – Energy Based Protein Structure Prediction
- ChemGenome 2.0 – Gene Prediction Software
- ViTO 20031125 – Protein Sequence Structure Alignments
- Phylo-mLogo 2.3 – Large-number Alignment Visualization Tool
- TFBSfinder – Yeast Transcription Binding Site Identification
- GS-Aligner 1.0 – Large-scale Pairwise Sequence Alignment
- SinicView 1.0.3 – Large-scale Alignment Visualization Tool
- PFAAT 2.0 – Multiple Sequence Alignments Analysis
- Indonesia 20050815 – Biological Sequence Analysis
- pdb_extract 3.11 – Prepare Data for Submission to the PDB
- sequins 20070909 – Validation of Sequence Assignment
- buccaneer 1.5 – Electron Density Interpretation/Protein Model Building software
- Nautilus 0.2 – Electron Density Interpretation/Nucleotide Model Building software
- MOLREP 11.0 – Molecular Replacement
- BLANC – Macromolecular Crystallography
- BALBES 1.1.5 – Molecular Replacement
- PEDIG – Pedigree Analysis suited for Large Population
- LDSO 1.02 – Linkage Disequilibrium with Several Options
- FLK – Detect Selection in Population Trees
- DemoDivMS 0.2 – Predict Genetic Diversity at Microsatellite DNA Marker
- DistMiss 1.0 – Compute Matrix of Genetic Distances between Populations
- QTLMap 0.9.0 – Linkage Analysis software to map QTLs in Outbred Populations
- MicroFamily 1.2 – Detect Flanking Region Similarities among different Microsatellite Loci
- QDD 2.1 – Select Microsatellite Markers and Design Primers
- ESSA – Analyse RNA Secondary Structure
- MultAlin 5.4.1 – Multiple Sequence Alignment
- DisplayFam 1999 – Protein Familly Viewer
- VAST – Vector Alignment Search Tool
- SIMPA 96 – Predict Secondary Structure of Proteins
- R’MES 3.1.0 – Finding Exceptional Motifs in Sequences
- RHOM – Research of HOMogeneous regions in DNA sequences
- RenBio 0.7d – Identify Gene and Protein Name in Textual Document
- SHOW 20111109 – Structured HOMogeneities Watcher
- OSS-HMM – Secondary Structure Predictions
- MuGeN 20060919 – Exploration of Multiple Annotated Genome Portions
- KASKAD 1.0.1 – Temporal Information Extraction about Genes from Text Corpora
- ESAP 4 – Predict Loop Conformation in Proteins
- DIYABC 1.0.4.46beta – Approximate Bayesian Computation for Inference on Population history
- JMS v1 – Evaluation of Diagnostic Status of Juxtaposed Microsatellite Systems
- BOTTLENECK 1.2.02 – Detect Recent Effective Population Size Reductions from Allele Data Frequencies
- GeneClass 2 – Genetic Assignment and First-Generation Migrant Detection
- FreeNA – Analysis of Microsatellite Dataset Harboring Null Alleles
- Aflpdiv 1.1 – Compute Comparable Measures of Diversity from AFLP Data
- Diston 1.0 – Analysis of Diversity for Haploid Data with Distances between Haplotyes
- Rarefac – Option of Rarefaction and Partitioning of Allelic Richness within Populations
- PermutCpSSR 2.0 – Measures of Diversity and Differenciation from Haploid Population Genetic data
- Hapstep 20010312 – Stepwise Analysis of Diversity for Haploid Data with Distance between Haplotypes
- Haplodiv – Diversity and Differenciation from Haploid Populationgenetic data
- Contrib 1.02 – Contribution of Each Population to Total Diversity
- FaMoz 200906 – Software for Parentage Studies
- DR_SEQAN 1.5 – Analyze RT and PR Sequences
- GMS-MP 1.0 – Gibbs Motif Sampler for Pare Correlation Model
- MultiScan – Motif Scan in Multiple Alignments with Background built from HtBackground
- HtBackground – Building a Heterogeneous Background Model for DNA Multiple Alignments
- CMF – Contrast Motif Finder
- GeneBASE – Estimate Gene-level Expression from Affymetrix Exon Arrays
- MotifBooster – Transcriptional Regulatory Motif Modeling and Discovery
- IsotopeCalculator 2 – Compute Isotopic Distributions for Large Proteins
- imCellPhen Alpha – Interactive Mining of Cellular Phenotypes
- R functions for cDNA array analysis – cDNA Microarray Analysis
- QuantileMap – Visualization of Compactlydemonstrate Multiple Distributions in Genomic Applications
- PWKmeans 1.0 – Penalize & weight K-means Extends the Target Function of K-means
- rGN – Ratio-adjusted Gene-wise Normalization
- QSB – Computational Tool for Genetical Genomics
- Gifi Array Analyzer 1.2 beta – Analysis of DNA Microarray data and Gene Functional Classification data
- TightClust 1.0 – Resampling Based Clustering Method for Microarray data
- CisModule 20051205 – De novo Discovery of Cis-regulatory Modules
- GEA – SAGE data analysis tool
- GeneNotes 1.0 – FireFox Extension of Collecting and Managing Biological Information
- CisModScan 20050417 – Scan for Cis-regulatory Modules given PWMs
- R-SVM 2.0 – Recursive Sample Classification and Gene Selection with SVM
- MultiModule 1.0 – de novo Discovery of Cis-regulatory Modules in Multiple Species
- MADS+ 20110328 – Discover Differential Splicing Events from the Affymetrix Exon Junction Array data
- SeqMap 1.0.13 – Map Millions of Short Sequences to Genome
- CisGenome Browser 1.1.3 – A Flexible Tool for Genomic Data Visualization
- JETTA 1.0.0 – Junction and Exon array Toolkit for Transcriptome Analysis
- SpliceMap 3.3.5.2 – Splice Junction Discovery Using RNA-Seq
- GEOSS 2.6.1 – Gene Expression Open Source System
- Ultrasome 1.0 – Detect Gains and Losses of Chromosomal Material in DNA copy-number data
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