2012 April
- WordCloud 1.0RC2 – Cytoscape plugin to Generate a Visual Summary of a Network
- Enrichment Map 1.2 – Cytoscape plugin for Functional Enrichment Visualization
- PTMClust 1.1 – A Post-translational Modification Refinement Algorithm
- LOLA 1.36 – Generate Sequence Logos using Position Weight Matrix based Protein Profiles
- BRAIN 1.0.5 /BRAIN Library 1.5 – Biologically Relevant Analysis of Interaction Networks
- NetMatch 1.0.1 – Cytoscap plugin to Query Networks for Patterns
- LigAlign 1.0 – Ligand-based Active site Alignment and Analysis
- Compo – Composite Motif Discovery
- TAMO 20120321 – Analyze Transcriptional Regulation using DNA-sequence Motifs
- LGSFAligner 01 – Align two RNA Secondary Structures Locally
- FindProbe v2 – Design Probes for Microarrays
- Spark 1.1.0 – Interactive Cluster Visualization Tool
- TMpred 1.0 – Prediction of Transmembrane Regions and Orientation
- BranchCut 1.0 – Break Long Branches in a Tree by Adding Taxa
- GenTree 0.5 – Generate Random Trees from a pure Birth Process
- RandomTaxa 1.0 – Select at Random Taxa from a Phylogenetic Tree and Output the reduced tree
- TreeCorrect 1.2b – Compute Percentages of Tree Correct or Correct Tree
- SuperTree 0.85b – Build Phylogenetic Supertrees
- MLtree 1.0 – Maximum Likelihood Model Estimation for Phylogenetic Trees
- MALDIPepQuant 3.1 – Quantify MALDI peptides (SILAC) from Phenyx output
- Make2D-DB II 3.10.2 – Gel Electrophoresis 2D-PAGE Databases
- IScan 1.0.0 – Search for Insertion Sequences (ISs), their Inverted Repeats (IRs), and associated Direct Repeats (DRs)
- HCD/CID spectra merger tool
- GMM – Detects Copy Number Variation from the Distribution of Copy Number Ratios
- find_max_cover – Determine the best Combination of Local Alignments to a Query Sequence
- SBRT 2.0.0 – The Systems Biology Research Tool
- GenomeHistory – tool to fully Sequenced Genomes
- ISA 1.0.0 – Iterative Signature Algorithm
- ExpressionView 1.00 – Explore Biclusters Identified in Gene Expression data
- Mapping Tool 1.3 – Map Different Nomenclatures
- Convert2Sbml / Convert2Matlab – Convert Metabolic Network Source files into SBML / MATLAB files
- efmtool 4.7.1 — Elementary Flux Mode Tool
- MtreeHMM 0.1.01 – Mutagenetic Tree Hidden Markov models
- icbn 0.2-13 – Isotonic Regression Conjunctive Bayesian Network models
- CT-CBN 0.1.04 – Continuous Time Conjunctive Bayesian Networks
- COILS 2.2 – Prediction of Coiled Coil Regions in Proteins
- BOXSHADE 3.2.3 – Pretty Printing and Shading of Multiple-Alignment files
- ALF 1.0 – Simulation Framework for Genome Evolution
- SloppyCell – system for Modeling Biochemical Reaction Networks
- BioHPC 1Rev293 – Computational Biology Application Suite for High Performance Computing
- MOIL 12.0.3923 – Molecular Modeling Software
- PROTARCH – Predict Protein Structure
- CluMa-GO 1.5 – Visualization of Mappings between the Gene Ontology and Cluster Trees
- MoMaVis 1.31 – Molecular Marker Visualization tool
- LAILAPS – Search Engine for Life Science data
- HTPheno – Image Analysis Pipeline for High-Throughput Phenotyping
- KGML-ED 1.0 – Edit, Process, and Visualize KGML pathway files
- MAVisto 2.7.0 – Motif Analysis and VISualisation TOolkit
- SMArrT – Normalisation of Expression Data in Files
- BATEx 0.1.2 – A Data Warehouse for Array-based Gene Expression Data of Plants
- SNP2CAPS – SNP and INDEL Analysis Tool for CAPS Marker Development
- Jstacs 2.0 – Java Framework for Statistical Analysis and Classification of Biological Sequences
- Meta-All 1.2 – Store and Access Information about Metabolic Pathways
- LABTOOLS 2.1 – Program for the Molecular Biological Lab
- Primer Factory 2.0 – Tool for Searching and Designing Primers
- BLASTER 1.2 – Tool for BLAST and Sequence Extractions in Batch Mode
- SI-FI 3.1 – RNAi (RNA interference) Off-target Prediction
- CentiBiN 1.4.3 – Centralities in Biological Networks
- MISA – MIcroSAtellite Identification Tool
- GLIEP – Navigation and Exploration of Interconnected Pathway Visualization
- MetaCrop – Browsing and Working with Information from the MetaCrop database
- CentiLib – Computation of network centralities
- DBE2 – Database for Biological Experiments
- Curator tool 3.1 – Annotate Biological Pathways based on the Reactome Schema
- Author tool 4.0 – Input data into Reactome
- PathwayLab 1.3 – Pathway Analysis tool
- nocoRNAc 1.23 – Predict & Characterise ncRNA Transcripts in Bacteria
- Mayday 2.13 – Microarray Data Analysis
- iPathways 1.2.1 – Biological Pathways on the iPhone
- Dunnart 2.0 – Constraint-Based Diagram Editor
- Adun 0.81 – Biomolecular Simulator
- ByoDyn 5.12 – Study of Biochemical Networks within the framework of Systems Biology
- SBW 2.9.0 – Systems Biology Workbench
- Athena r4 – Modular CAD/CAM software for Synthetic Biology
- SWAP 0.9 – Analyse Genetic Parameters in Half Sib Families
- PaupUp 1.0.3.1 – Graphical Frontend for Paup* DOS software
- Micro-Checker 2.2.3 – Microsatellite Data Checking Software
- mesquite 2.75 – Modular System for Evolutionary Analysis
- MacClade 4.08a – Phylogenetic Analysis
- BmpFrame 0.01 – Draw a Frame with Tick Marks around an 8-bit Bitmap
- dotplot 0.3 – Simple Shaded DotPlotter
- RC – Reverse/Complement
- ResampleSeq – Sequence Resampler
- cswA 0.01 – Conserved Seq Window Annotater
- txgen 0.1 – PAUP Text Generator and Parser
- Fas2Nex – .FAS to .NEX converter
- SDSW 0.03 – Sliding Divergence Sequence Window
- FAMD 1.25 – Dominant Fingerprint Data Handling and Analysis
- ApE 2.0.44 – A Plasmid Editor
- Fatsim – Simulate the Effect of extracting/not extracting lipids on the outcome of stable Isotope Mixing Models
- AFLPdat 20100624 – Handling of Dominant Genotypic data
- McQSAR 1.2.3.74 – Generate Quantitative Structure-activity Relationships
- Bodil 0.8.1 – Biomolecular Visualization and Modeling
- FINESSE – Incorporate Regressive Models into the VITESSE likelihood engine
- VITESSE – Rapid exact Multilocus Linkage Analysis via Genotype set-recoding and Fuzzy Inheritance
- ZAPLO 2.1 – Zero-recombinant Haplotyping
- WhichRun 4.1 – software for Assigning Individuals to Populations
- WHICHPARENTS 1.0 – Use Mutlilocus Genotype data to Determine the Most likely Parents of Offspring
- WHICHLOCI 1.0 – Use Genotype data to Identify the loci most useful for Population Assignment
- RepeatRunner – Repeat Identification and Masking in Dipterans
- CGL 0.08 – Library designed to Facilitate the use of Genome Annotation
- TWOLOC – Analyze Two-locus Susceptibility Gene Models in affected Sib-pair data
- rapier 0.1 – T test on pairs of Array Experiments
- wclique 0.1 – Genetic Marker Selection program
- TreeView 1.66 – Cluster Results Visualization Software
- Consel 0.20 – Assess Confidence of Phylogenetic Tree Selection
- TripleC – Constuct Consensus Trees from Rooted Triples
- TAXNAMECONVERT 2.4 – Rename Sequence and Taxon names in Tree and Sequence files
- SISSI 1.0 – Simulating Sequence Evolution with Site-Specific Interactions
- SIMULATOR 1.0 – Simulate DNA and Protein datasets with well-defined Insertion-deletion dynamics
- REvolver 1.0 – Modeling Sequence Evolution under Domain Constraints
- IPHULA / pIPHULA 1.16 – Inference of Population History Using a Likelihood Approach
- PhyNav 1.0 – Reconstruct Evolutionary Relationship among Contemporary Species based on Genetic data
- PDA 0.5.2 – Phylogenetic Diversity Analyzer
- Parat 0.9.1 – Estimates Site Specific Substitution Rates from a set of DNA sequences
- NGV 0.1 – Browser for Efficient Display of Large HTS Data Sets
- mrc.py 1.0 – Compatibility Lengths of Supertrees and Gene Trees
- misfits 1.0 – Evaluate Goodness of Fit between Phylogenetic Model and Alignment
- MASon rev12 – Reduce the Computing Time of NGS Analysis Pipelines
- HGT – Simulate and Estimate Horizontal Gene Transfer events
- GeoMeTree 1.1 – Geodesic Metric on Trees
- EMOGEE 20070704 – Estimator for MOdels of Gene Expression Evolution
- ALIFRITZ 1.0 – Statistical Multiple Alignment and Phylogeny Reconstruction
- IQPNNI 3.3.2 – Reconstruct a Phylogenetic Tree based on DNA or Amino Acid Sequence data
- MrBayes 3.2.1 – Bayesian Inference of Phylogeny
- CALIB 1.2.0 – Estimate absolute Expression levels from two color Microarray data
- SIBR 0.95 – Normalization of DIGE data containing Region-based Intensity Biases
- QDB 1.1 – Query Driven Biclustering
- SynTReN 1.2 – Generator of Synthetic Gene Expression data for Design and Analysis of Structure Learning algorithms
- DISTILLER 2.0 – Data Integration System To Identify Links in Expression Regulation
- ViTraM 2.0 – Visualization of Transcriptional Modules
- COMODO 1.0 – Identify Conserved Coexpression Modules between Organisms
- MotifSampler 3.2 – Probablistic Motif Detection Approach based on Gibbs Sampling
- ModuleDigger – An Itemset Mining framework for the Detection of Cis-regulatory Modules
- CRoSSeD 1.1 – Motif Screening based on Structural features
- ReMoDiscovery – Inferring Transcriptional Module networks from ChIP-chip-, motif- and microarray data
- Endeavour / HIGHFLY 2.44 – Prioritization of Candidates Genes
- TOUCAN 3.1.0 – Regulatory Sequence Analysis on Metazoan Genomes
- GAPIT – Genome Association and Prediction Integrated Tool
- Phylogeographer 1.1 – Evaluate Genetic and Geographic Interactions
- GDPC 2.0 – Access to Genomic Diversity and Phenotype data
- TASSEL 4.0 beta – Association And Diversity Analyses In Plants And Animals
- SVA 1.10 – Sequence Variant Analyzer
- FPG 1.0 – Full Parental Genotyping
- CoNe 1.01 – Estimate Ne from two temporal samples
- SNPPIT 1.0 – Perform Fast and Accurate, Likelihood-based, Parentage Inference with SNPs
- SPIP 1.0 – Simulate Pedigrees and Genetic data in Age-structured Population
- SPAM 3.7b – Genetic Stock Identification Software
- SNPLINK – Multipoint Linkage analysis of Densely Distributed SNP data
- SNP HiTLink 1.5.1 – SNP High-Throughput Linkage Analysis System
- SNPALYZE 8.0 – SNP and Disease Association Analysis Software
- SNIPPEEP r1 – Visualise Results from whole Genome Genotyping
- SNaP – Simulation of sNp haplotype data And Phenotypic traits
- SNAP Workbench 2.0 – Analysis programs for making Inferences on Population processes
- LBL 1.0 – Find Association of SNP Haplotype
- DIME 1.0 – Identifying Differential ChIP-seq Based on an Ensemble of Mixture Models
- rGLM 1.1 – Generalize Linear Modeling with Regularization for Case-control Association Studies
- TopKCEMC 1.1 / TopKSpace 1.0 – Rank Aggregation Tool
- MC-PDT 0.2.2 – Linkage Disequilibrium Test
- miRComp – Composite MicroRNA Target Prediction
- DE-SAGE – Analyze SAGE Library data
- Pathway – Heritable Clustering Algorithms
- tagSNPfinder – Mutilocus LD Measure and Tag SNP Selection
- DNC-MIX – Model Distribution of Gene Expression Profile of Test Sample as Mixture of Distributions
- CSI – Construct Confidence set of Markers within prespecified Genetic Distance from the Disease Locus
- MAXPROC – Calculate Maximum Likelihood Estimates of Linkage Parameters
- START – Find Starting Points for MCMC analysis
- SIMPLE – Sequential Imputation for MultiPoint Linkage Estimation
- Mr T – Tomography software written in Python.
- JAMES 1.0b – JEOL Automated Microscopy Expert System
- SAVR 20050411 – Semi-Automated Virus Reconstruction
- Gorgon 2.1.1 beta – Molecular Modeling system
- MismatchHetMutRate – Perform Mismatch Analyses allowing for Heterogeneity of Mutation Rates
- LAPD – Estimate Maximum Likelihood Allele and two-locus Haplotype Frequencies
- SAMOVA 1.0 – Define the Genetic Structure of Population
- ABCtoolbox – Toolkit to perform Approximate Bayesian Computations
- SPLATCHE 2.01 – Simulate Genetic Diversity taking into Account Environmental Heterogeneity
- fastsimcoal 1.1.2 – Continuous-time Coalescent Simulator of Genomic Diversity
- AQUASPLATCHE 1.0 – Simulate Genetic Diversity based on a Realistic Vectorized Environment
- SIMCOAL 2.1.2 – Simulation of Molecular data in interconnected Populations with Arbitrary Demography
- silcLOD – Calculate Nominal Significance Levels and Critical LOD Scores
- Scola-Gen 1.0 – Simulation Model of Population Genetic Processes
- Eco-Gene 1.0 – Combine Population Genetic and Population dynamic processes with Forest Growth Models
- CoTrix 3.0 – Analysis of complex DNA Banding Patterns
- SGS 1.0d – Analysis of Spatial Genetic and Phenotypic Structures of Individuals and Population
- SASQuant 1.3 – Analysis of Quantitative Genetic Data
- SASGene 1.2 – Gene Segregation and Linkage analysis in Breeding Population
- RvTests v1 – Rare Variants TESTS
- snp.plotter 0.2.1 – SNP/haplotype Association and Linkage Disequilibrium plotting package
- R/qtlDesign 0.91 – Software for QTL Experimental Design
- Rmetasim 1.1.12 – METApopulation SIMulation
- R/gap 1.1-3 – R/Genetic Analysis Package
- CGR 1.0-5 – Classic Genetics in R
- FEST 0.0.6 – Simulations and Likelihood Calculations of Pair-wise Family Relationships
- SERIAL CLONER 2.5 – DNA Cloning, Sequence Analysis & Visualisation
- AnnHyb 4.946 / PyAnnHyb 0.021 – Manage Nucleotide Sequences
- RISCALW 1018 – Risk Calculation in Families with Duchenne Muscular Dystrophy
- RelativeFinder 20100813 – Check Relationships between pairs of Individuals
- QU-GENE 2.2.04 – Investigation of the Characteristics of Genetic Systems
- QUANTO 1.2.4 – Computes Sample Size or Power for Association Studies
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