2011 June
- AFINITI 1.0 – Volumetrics Measurement of Human Brain Tumor
- GCellIQ 1.0 – Genomic Cell Image Quantitator
- DCellIQ 1.0 – Quantitative Time-lapse Nuclei Image Analysis
- NeuriteIQ 1.0 – Quantitative Neurite Image Analysis
- NeuronIQ 1.5 – Quantitative Neuron Image Analysis
- ZFIQ 1.0 – Quantitative Zebrafish Image Analysis
- AxonTracker 1.0 – Track and Label Axon Structures
- BDB 0.91 – Deformable Curve in n-dim
- VANO 1.741 – 3D Image Annotator
- CellExplorer 1.0 – 3D C. elegans atlas Building & Application Tools
- TinyQuant v1.55 – Gel Image Analysis
- WinIAP – Ion Activities and Calcite Saturation Index
- Chemulator – Converter for Chemical Concentrations
- PersonalGenBank 200610 – Local Sequence Database
- Align 200807 – DNA Sequence Alignment Editor
- SeqAssem 200807- Molecular Sequence Assembly
- ColorDecontmas 1.00 – ImageJ macros for Color Deconvolution for TMA images
- TMAJ 3.4.0 – Tissue MicroArrays Information & Image Analysis Software
- Gel Analyzer 2010a – 1D Gel Electrophoresis Image Analysis
- CP ATLAS 2.0 – Thin Layer and Gel Analysis Software
- CoStat 6.4 – Statistics Software
- CoPlot 6.4 – Software for Great Scientific Graphs, Maps, and Technical Drawings
- AngioQuant 1.33 – Quantification of Angiogenesis through Image Analysis
- MAmodel 20060511 – Microarray Simulator
- ECN 20050107 – Expression Annotation of Copy Number
- CGH-Plotter 20051025 – MATLAB Toolbox for CGH-data Analysis
- CellLine – Stochastic Cell Lineage Simulator
- SGN Sim – Stochastic Genetic Networks Simulator
- SIMCEP 1.0 – Cell Image Simulator
- CellC 1.2 – Quantification of Labeled Bacteria by Automated Image Analysis
- Peak Explorer 2.11 – Automatic Processing of Spectra
- Graph Digitizer 2.16 – Digitization of Orthogonal Graphs
- WinDig 2.5 – Image Data Digitizer
- GPeriodic 2.0.10 – Look up Data of Elements from the Periodic Table
- G3data 1.5.4 – Extract Data from Graphs
- UnGraph 5 – Digitizer Program Which Gives X,Y Coordinates of Lines or Points on Scanned Images
- Stat-200 2.1 – General Statistics and Graphics Package
- FigSys 2.4 – Publication Quality Graph Plotting and Data Analysis
- Ileum 3.0 – Isolated Guinea-Pig Ileum Simulator
- CardioLab 3.0 – Simulation of in vivo Cardiovascular Pharmacology Experiments
- NeuroSim 4 – Neurophysiology Simulations
- EnzFitter 2 – Curve Fitting & Analysis of Enzyme Kinetics Experiments
- CalcuSyn 2 – Dose-effect analysis
- AssayZap 3.0 – System for Analyzing RIAs, ELISAs, IRMAs and other Assays
- QuantiScan 3.0 – Densitometry using Ordinary Office Scanners
- Phoretix 1D / Phoretix 1D Pro – 1D Gel Analysis
- MELANIE VIEWER 7.0 – Visualize Gels and Related Data obtained from Melanie
- Melanie 7.0 – 2D Gel Analysis Platform
- CMEIAS Color Segmentation 1.0 – Segment & Analyze Foreground Objects within Complex Images
- CMEIAS 1.27 – Microbial Ecology Image Analysis Software
- Leaphy 1.0 beta – Phylogenetic Tree Estimation Software
- JEBL 0.4 – Java Evolutionary Biology Library
- PSI Protein Classifier 1.0.1.49 – Automation of the PSI-BLAST Results Analysis
- Blast Parser v1.2.6.14 – The Excel Style Viewer for Blast Output
- PoInTree 1.0.1.2 – Polar and Interactive Phylogenetic Tree
- DoubleTree 0.7 – Compare Two Trees using Coupled Interaction
- TaxonTree 1.2 – Interactive Tree Visualization for Kingdom Animalia
- TreePlus 20060630 – Explore Large, Complex Food Webs
- EcoLens 20051212 – Browse through a Large Database of Information about Food Webs
- Trebol 20110311 – Interactive Comparative Genomics Tool
- B3 3.31 – Bibliography Base for Biologists
- Baobab 3.31 – Editor for Large Phylogenetic Trees
- TreeDyn 198.3 – Dynamic Graphics & Annotations for Phylogenetic Analyses
- CDTree 3.1 – Protein Domain Hierarchy Viewer and Editor
- ReadSim 0.12 – Simulator for Sanger and 454 Sequencing
- OSLay 1.0 – Optimal Syntenic Layout of Unfinished Assemblies
- Metasim 0.9.5 – Sequencing Simulator for Genomes and Metagenomes
- MEG2DIST – Compute Ecological Indices for Multiple Metagenomic Datasets
- LOCAS / SUPERLOCAS – Low-coverage Short-read Assembler
- Crosslink 1.2.6 – Visualization & Exploration of Sequence Relationships between (micro) RNAs
- Darwin Rocks 1.0.3 – Evolution of Music
- Vmatch – Large Scale Sequence Analysis Software
- CGViz 1.3.5 – Viewer for Biomolecular Data
- Squint 1.02 – Multiple Sequence Alignment Editor
- Pebble 1.0 – Phylogenetic Analysis Application
- SHiAT 1.1 – Generates Plots of Variation along Sequence Alignment
- BaTS 1.0 – Measure and Test Phylogeny Trait Associations
- Adapt-A-Rate 1.0 – Estimate the Rate of Adaptive Fixation in a Population
- Genie 3.0 – Estimating Demographic History from Molecular Phylogenies
- Contevol 1.01 – Continuous Character Evolution Teaching Program
- PopG 3.3 – Genetic Simulation Program
- Dnatree 1.3 – DNA Phylogeny Teaching Program
- TreeMe 200807 – Visualization, Editing and Annotation of Phylogenetic Trees
- SequenceJuxtaposer 1.2 – Browse and Compare Gene Sequences
- TreeJuxtaposer 2.1 – View a Single Tree, or Compare Two or more Trees
- Mac5 1.7.3 – Phylogenetic Reconstruction using Gapped Data
- Conserve IV 1.4b – Assess & Prioritorize Conservation Schemes based on Phylogenies
- TreeMaker 1.3 – Interactive Building of Taxonomies
- Multilocus 1.3b – Analysis of Multi-locus Population Genetic Data
- MESA 1.9.23 – Macroevolutionary Analysis & Simulation
- TreeEdit 1.0a10 – Organize, View & Manipulate sets of Phylogenetic Trees
- TreeStat 1.2 – Calculate Summary Statistics of a set of Trees
- Tracer 1.5 – Analyse Results from Bayesian MCMC programs such as BEAST & MrBayes
- Se-Al 2.0a11 – Manual Sequence Alignment Editor
- Path-O-Gen 1.3 – Explore Temporal Signal & Clocklikeness in Molecular Phylogenies
- FigTree 1.3.1 – Produce Figures of Phylogenetic Trees
- Phylogen 1.1 – Simulate Phylogenies
- VisSPA 1.62 – Calculate Frequency of Residues
- VarPlot 1.2 – Similarity Plotting for Alignment of Sequences
- SimPlot 3.5.1 – Sequence Similarity Plotting
- MargFreq 1.02 – Calculate Marginal Frequencies at each Position of a Nucleotide/Amino Acid Sequence
- CleanCollapse 1.0.5 – Transfer Alignment of Sequences into Single Sequence
- NimbleTree 2.6 – Make Phylogenetic Trees from Sequence Data
- JColorGrid 1.860 – Transform Numerical or Text Data into Color-grids
- PI 2.0 – Test the Assumption of Phylogenetic Independence
- covarionTest 20050610 – Covarion Structure Test
- BADGER 1.02 beta – Bayesian Analysis of Phylogenies
- BAMBE 4.01a – Bayesian Analysis of Phylogenies
- PVT – Phylogenetic Visualization tool
- STC 1.2 – Reconstruct Large Phylogenies
- ProfDistS 0.9.9 beta – Construction of Large Phylogenetic Trees
- PCAGEN 1.2.1 – Perform Principal Component Analysis on Gene Frequency Data
- FSTAT 2.9.3.2 – Estimate & Test Gene Diversities
- T-REX 4.01 – Reconstruct Phylogenetic Trees and Reticulation Networks
- REAP – Manipulation & Phylogenetic Analysis of Restriction Data
- FastME 2.0.7 – Fast & Accurate Phylogeny Reconstruction
- GEODIS 2.6 – Nested Clade Phylogeographic Analysis
- PAL 1.5.1 – Java Library for Molecular Evolution & Phylogenetics
- TREECON 1.3b – Construction & Drawing of Evolutionary Trees
- tree-puzzle 5.2 – Maximum Likelihood Analysis
- TreeViewJ 1.1.2 – View & Analyze Phylogenetic Trees
- COMPONENT 2.0 – Analysis of Evolutionary Trees
- GeneTree 1.3 – Compare Gene and Species Trees
- NDE 0.5.0 – NEXUS Data Editor
- Rainbow beta 1.2 – Toolbox for Phylogenetic Supertree Construction & Analysis
- Supertree 0.3 – Construct Supertree
- TreeViewX 0.5.1 – Program to Display Phylogenetic Trees
- TreeView 1.6.6 – Tree Drawing Software
- Phylip 3.69 – Free Package of Programs for Inferring Phylogenies
- abi2xml 1.2 – Convert Abi Trace File to Xml File
- TreeSAAP 3.2 – Selection of Amino Acid Properties using Phylogenetic Trees model
- BioCocoa 2.2.2 – Cocoa Framework for Bioinformatics
- Vised 1.1 – Sequence Editor / Display Software
- Methyl Primer Express 1.0 – Design PCR Primers for Methylation Mapping Experiments
- Primer Prim’er 5.6.0 – PCR Primer Design Tool
- seqjoin – Predict Complete cDNA Insert Sequence
- Clone Manager 0.1 – Cloning and Protein Expression LIMS
- ORFprimer 1.6.4.1 – High Throughput PCR Primer Design
- ORFer 1.3.2.2 – Retrieval of Protein Sequences and Open Reading Frames from GenBank
- AutoDimer 1.0 – Screening Tool for Primer-dimer & Hairpin Structures
- PCRsetup – Tool for Planning PCR and qPCR Reactions
- NetPrimer – Free Primer Analysis Software
- Protein Investigator 3.0.2 – Simulation of Protein Folding
- CTB 2.0 – Educational Aid for Biology or Medicine
- Digital Frog 2.5a – Virtual Frog Dissection, Anatomy & Ecology
- ScienceMatrix – Cell Structure and Function
- Hands On Genetics – Interactive Education Programs of Genetics
- Virtlab 1.3 – Simulate Molecular Biology Laboratory
- Photosynthesis – Teach Photosynthesis
- Molecular Basis of Medicine – Introduction to Molecular Biology
- Diffusion Simulator – Simple Diffusion Random Walk Simulation
- vExplorer 2.0 – Function Explorer
- Ilya – Reaction-Diffusion Simulator
- Linear Pathway Simulator – Control Parameters of the Pathway & Study the Response
- Quasar 1.2 – Score & Rank Sequence-structure Alignments
- HALO 1.3 – Precise RNA de novo Transcript Half-life Determination
- FERN 1.4 – Stochastic Simulation & Evaluation of Reaction Networks
- BioWeka 0.6.1 – Weka Framework for Bioinformatics
- ProCope 1.2 – Protein Complex Prediction and Evaluation
- ProteinVis 2.1.6 – Tree viewer for Hierarchical Clusterings of Proteins
- MeltDNA 1.0.1 – DNA Hybridization & Melting Thermodynamics Prediction
- HBNG 1.0 – Hydrogen Bond Network Graph
- HBAT 1.1 – Hydrogen Bond Analysis Tool
- ProTag 1.4 – Office Add-In for offering SmartTag of Protein
- PAT 0.9 – Protein Alignment Tool
- PIVOT 2.0 – Protein Interactions VisualizatiOn Tool
- PHIRE 1.00 – Reveal Regulatory Elements in Bacteriophage Genomes
- STORM 1.01 – Protein Analyses of BLAST, FASTA, Pfam and ProtParam
- Q5 – Classification of Complete Mass Spectra of a Complex Protein Mixture
- NASCA 20110516 – Side-chain Resonance Assignment & NOE Assignment
- DISCO 1.0 – Structure Determination of Protein Homo-oligomers
- RDC-PANDA 1.0 – NMR NOE Assignment & Protein Structure Determination
- Osprey 1.2.0 – Protein-protein Interaction Networks Visualization System
- MPtopoQuerier – Search Database of Membrane Proteins
- MPEx 3.2 – Tool for Exploring Membrane Proteins
- VHMPT – Viewer & Editor for Helical Membrane Protein Topologies
- PSAAM – Protein Sequence Analysis And Modelling
- Ebbie 3.0.9 – Analysis & Storage of Small RNA Cloning Data
- Ebbie-MM 4.3 – Analyze Single Mismatches of Small RNAs to the genome
- RNA-DV 1.0 – Design & Visualization Tool for RNA Secondary Structure
- FSFinder 2.0 – Predict Frameshifting in Genomic Sequences
- PRI-Modeler 1.3 – Extract RNA Structure elements from PDB files of Protein-RNA Complexes
- InterViewer 4.0 – Visualize Large-scale Protein Interaction Networks
- PseudoViewer 3.0 – Visualization of RNA Pseudoknots of any type
- TRFolder – Telomerase RNA Structure Prediction
- RNAv – Search Genomes for RNA Secondary Structure Variation
- RNATOPS 1.2 – RNA Pseudoknot Search in Genomes
- RNApasta 1.01 – RNA Structural Alignment & Statistical Analysis
- miRanda 201008- microRNA Target Detection Software
- Gardenia – Compare & Align RNA Structures
- RNAfamily – Java Viewer for RNA Secondary Structures
- Carnac 0.98 – Predict Secondary Structure for a set of Homologous RNA Sequences
- Rnall 2.0 – RNA Local Secondary Structure Prediction
- RnallViewer 1.0.1 – RNA Analysis Visualization Tool
- XRNA 1.2.0b – Creation, Annotation & Display of RNA Secondary Structure Diagrams
- RnaViz 2.0 – Secondary Structure Drawings of RNA Molecules
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