2011 October
- motifdraw – Graphically Represent Motifs
- Mclip – Motif Detection based on Cliques of Profile-profile Alignments
- SSalign – Secondary Structure Determination in DNA/RNA Sequences
- HMMAccel – Speeding up HMM-searches
- JTreeView 0.8 – Java based Phylogenetic Tree Viewer
- Java Treeview 1.1.6r2 – Gene Expression Visualization Tool
- BlatView – Mapping EST’s to Genomes
- AlnEdit 1.0 – Fast and Memory Efficient Alignment Editor
- PhyloGenie – Automating Phylome Analyses
- CLANS 20101007 – Visualize Protein Families based on Pairwise Similarity
- I-TASSER 1.1 – Protein Structure & Function Predictions
- FFAS 03 – Pretein Structure Prediction based on Profile-profile Comparison
- DisEMBL 1.5 – Protein Disorder Prediction
- TRUST 1.0 – Repeat Detection Method
- HHrepID 1.0.0 – de novo Protein Repeat Detection
- InteroPorc 2.0.2 – Automatic Molecular Interaction Predictions
- NOXclass – Prediction of Protein-protein Interaction Types
- InterEvol PyMOL Plugin 1.0 – Structure-oriented Exploration of Sequence Alignments
- Flex-EM – Fitting and Refinement of Atomic Structures
- ModPipe 2.2.0 – Calculate Protein Structure Model
- SAPTF 1.7 – Sequence Analysis Plugin Tool Framework
- APAT 1.4.1 – Automated Protein Annotation Tool
- AVP 1.3 – Calculate Protein Void Volumes and Packing Quality
- Torsions – Calculates Backbone Torsion Angles from a PDB file
- NW 3.12 – Pairwise Needleman and Wunsch Sequence Alignment program
- MINT 3.2 – User Interface to Modeller
- QTree 2.3 – Graphics Rendering using Quad-tree Algorithm
- ProFit 3.1 – Protein Least Squares Fitting
- CS-PSeq-Gen 1.0 – Simulation of Protein Sequences under Constraints
- PDBpy – Python Parser for PDB files
- RNA – RNA Consensus Secondary Structure Prediction Software
- XtalView 4.0 – Molecular Graphics Program
- CONSCRIPT – Generate Electron Density Isosurfaces in Protein Crystallography
- XmMol 3.1 – Macromolecular Visualization and Modeling tool
- YAKUSA – Scan Structural database with Query Protein Structure
- JaDis – Compute Distances between Nucleic Acid Sequences
- BARCOD 1.0 – Multiple Alignment
- Opscan – Comparing Genomes
- MPB – Metabolic Pathway Builder
- MixNet 1.1.2 – Analyzes Biological Networks using Mixture Models
- seq++ 4.2.0 – Library of Sequence Statistics
- MetaViz – Visualization software for Metabolic Network
- SMILE 1.47 – Structured Motif Inference and Evaluation
- RISO – Motif Discovery Tool
- PRIAM 201105 – Sequence Profiles Generated from the ENZYME database
- MareyMap 1.0 – Recombination Rate Estimator
- GNA 8.1 – Modelling & Simulation of Genetic Regulatory Networks
- FamFetch 2.0 – Search for Tree Patterns in Databases of Phylogenetic Trees
- MFPaQ 4.0.0 beta5 – Parse, Validate, and Quantify MS Proteomics Data
- Paris 2.0 – Manage and Analyse Data from 2D Electrophoresis Proteomic Image
- OVNIp 1.4 – Facilitate the Analysis of Mass Spectrometry Data
- Sarment 4 – HMM Sequence Partitioning and Maximal Predictive Partitioning
- PSbR – Test Evolution and Conservation of Common Clusters of Genes
- MOTUS 1.1.3 – Motif search in Metabolic Networks
- Migal 2.2 – Compare RNA Secondary Structure
- DCJ2HP – Bayesian Sampling of Genomic Rearrangement Scenarios via Double Cut and Join
- Genepi 2.0 – Genome Annotation
- C3Part/Isofun – Local Alignement of two or more Graphs Representing Biological Data
- C3P/CCCPart – Merging Two or More Graphs Representing Biological Data
- Cravela – Identify and Evaluate miRNA Regulatory Modules
- BaobabLuna 1.1 beta – Manipulation of Signed Permutations in the Context of Genomic Evolution
- QUERY_WIN – Retrieval Program with Graphical User Interface for ACNUC Databases
- Seqinr 3.0 – Biological Sequences in R
- Alfacinha – Simulation of Sequence Evolution with Neighbouring-site Dependencies
- Cassis 1.0 – Detect Genomic Rearrangement Breakpoints
- Plasmidomics 0.2 – Plasmid Drawing Program
- Rasmol 2.7.5.2 – Molecular Graphics Visualisation
- GenoFrag 2.1 – Design Primers Optimized for Whole Genome Scanning by Long-range PCR Amplification
- BVTech Plasmid 5.1 – DNA Sequence Analysis & Plasmid Drawing Software
- IThOS 2.1 – Tool for Designing Oligonucleotide Primers
- PLAST 1.0 – Parallel Local Alignment Search Tool for Database Comparison
- GASSST 1.28 – Global Alignment Short Sequence Search Tool
- BioMAJ 1.2.0 – Workflow Engine Dedicated to Data Synchronization and Processing
- OxyGene 1.1.0 – Investigate Oxidative-response Genes in whole Prokaryotic Genomes
- TRANS-MNET 20070315 – Time Series Analysis of Gene Expression Profiles
- ArrayCluster 1.0 – Mixed Factors Analysis of Microarray Gene Expression Data
- SiGN-SSM 1.0.2 – Gene Network Estimation Software
- DA 1.0 – Estimate Unknown parameters in a Pathway Model
- TotalLab Quant 12 – Analysis Tools for Quantitative Image Analysis
- CADLIVE 2.75 – Computer-Aided Design of LIVing systEm
- SwarmPS 0.9.3 – Particle Selection from Electron Micrograph Data set
- Cell Illustrator 5.0 – Platform for Systems Biology
- iCluster 1.05 – SubCellular Localisation Image Visualiser
- Illoura 0.9 – Analysis, Visualization of Cellular and other Spatial Biological data
- IUPred – Predict Intrinsically Unstructured Regions of proteins
- Anchor – Predict Binding Regions in Proteins
- THREADER 3.51 – Protein Fold Recognition by Threading
- MEMPACK – SVM Prediction of Membrane Helix Packing
- MEMSAT 3 – Transmembrane Protein Structure Prediction
- GPGPUFRAGFOLD 0.1 – CUDA Fragment Assembly Based Protein Structure Prediction
- DISOPRED 2.43 – Intrinsic Protein Disorder Prediction
- CRC64 2006 – Improved 64-bit Cyclic Redundancy Check for Protein Sequences
- BioRAT 2.0 – Information Extraction for Biological Research
- HMMTOP 2.9 – Predict Transmembrane Helices and Topology of Proteins
- Topcons – Consensus Prediction of Membrane Protein Topology
- Phobius /PolyPhobius 1.05 – Combined Transmembrane Topology & Signal Peptide Predictor
- CoBaltDB 1.0 – Complete Bacterial and Archaeal Orfeomes Subcellular Localization Database
- MONKEY 2.0 – Identify Matches to DNA Motifs in Multiple Alignments
- ProBias/BIAS – Detect Compositional Bias in Biological Sequences
- NucImport – Nuclear Protein Import and Localisation Signals Predictor
- RactIP 0.0.2 – Joint Secondary Structure Prediction
- IPknot 0.0.2 – RNA Secondary Structure Prediction including Pseudoknots
- MultiLoc2 20091026 – Predict Animal, Plant and Fungal Protein Subcellular Localization
- SherLoc2 20091026 – Predicting Protein Subcellular Localization
- ProCon 1.1 – Localization & Visualization of Protein Conservation
- TESTLoc – Protein Localization Prediction based on ESTs
- SLML Tools v1.5.2 – Implement Generative Models of Subcellular Location
- Discriminative HMMs – Find Discriminative Motif to Predict Protein Subcellular Localization
- NQ-Flipper 2.7 – Validate Asparagine and Glutamine Side-chain Amide Rotamers in Protein Structures
- TopMatch – Protein Structure Alignment
- ProSa 2003 – Protein Structure Research Tool
- Wise 2.2.0 – Compare Protein Sequence to Genomic DNA Sequence
- Pratt 2.1 – Find Flexible Patterns in Unaligned Protein Sequences
- cPath 0.7 Beta – Pathway Database Designed for Systems Biology Research
- MMPRO 0.7 – Molecule Visualization & Analysis Program
- Jamberoo 11 – Cross-Platform Molecular Editor & Builder
- MaSK 1.3.0 – Molecular Modeling and Simulation Kit
- ViewMol3D 5.00.alpha.3 – 3D OpenGL Viewer for Molecular Structures
- MDR-Phenomics 1.0 – Detect Gene-gene Interaction in the Pedigree Data
- seqEM 1.0 – Genotype Calling Algorithm for Resequencing Data
- CAPL 4.1.8 – Combined Association in the Presence of Linkage
- GWAS-NR 2.0 – noise-reduction GWAS analysis
- XQTL 1.0 – Gamily-based Allelic/Haplotype Association Test
- X-LRT 1.0 – Estimate Genetic Risks and Test Association with X-linked Markers
- SIMLAPLOT 1.0 – Visualize Genotype and Phenotype Relationship
- SIBLINK 3.0 – Multipoint Linkage Analysis
- PDT 5.1 – Test for Linkage and Association in General Pedigrees
- OSACC 1.0 – Evaluate Evidence for Association in the presence of Genetic Heterogeneity
- OSA 2.1 – Ordered Subset Analysis Program
- GATOR 1.0 – Genetic Association Tests Based on Ranks
- EMK 1.0 – Extended Monks and Kaplan
- Combined_LRT 1.0 – Combined Likelihood Ratio Test for Candidate Gene Studies
- APL-OSA Beta – Identify Genetically Homogenous Subset of Families
- CNVAnalyst – Statistical, Bioinformatic, and Visual Analyses of CNVs
- APL 1.1 – Association in the Presence of Linkage
- APE 1.0 – Allelic Path Explorer
- HIPPO 1.0/ AEML 1.0 – Estimate Population Haplotype Frequencies from Pooled SNP data
- popgen 1.0 – R package for Statistical and Population Genetics
- CHIAMO 0.2.1 – Genotype Calling Algorithm for Multi-cohort Study
- FIXFCS 1.0 – Bug Fix for FCS Data Copy
- ZeissToSGI 1.1 – Convert Zeiss AxioVision TIFF files to files that can be read by SoftWoRx
- TweenMotif 1.1 – Visualize Locations of a Specified Target Motif
- FCSViewer 2.0 – Decompresses FCS data files for Display
- FCSExtract 1.02 – Extracts Flow Cytometry data from binary FCS files
- psi-square 1.2 – Search the Space of Gene Vectors
- PeakFinder 1.0 – Find Cohesin Binding Sites in Yeast ChIP Microarray Data
- LombScargle – Detect Periodic Patterns in Unevenly-spaced Data
- greylag 0.2.2 – Tandem Mass Spectrum Peptide Identification and Validation
- GADIST – Determine Best Distance Metric for Genome Analysis
- MoSART pr – NMR-based Biomolecular Structure Computation
- BlurLab 0.9 – 3D Simulated Microscopy Software Package
- PROTEAND 1.0 – Display Macromolecular Structural Uncertainty
- M-BISON 1.0 – Microarray-Based Integration of data SOurces using Networks
- SAGAT 1.0 – Svd Augmented Gene expression Analysis Tool
- ProtoMol 3.3 – Molecular Dynamics (MD) Simulation
- FCAnalysis 1.0.0 – Independent Component Analysis for Mining Gene Expression Data
- ViewCommonPaths – Visualization of Sequences with the Same Start and End Elements
- MD Morphing 1.0 – Perform Molecular Dynamics Morphing Simulations
- Sequoia 1.0.1 – Align Hpmologous Protein Sequences and Structures
- Bionet 3.0a – Biological Cell Network Pathway Simulation
- AlphaMol 1.0 – Tools for Biomolecular Geometry
- noRNAlize 1.0 – RNA SHAPE Data Normalization software
- LoopTK 2.0.1 – Protein Loop Kinematic Toolkit
- iFBA – Integrated Flux Balance Analysis Model of Escherichia coli
- DNA Chromatogram Explorer Lite 3.2 – View, Edit & Convert Chromatogram
- Seqool 3.1 – Search Biological Signals in Nucleic Acid Sequences
- AlloPathFinder 1.1 – Compute Likely Allosteric Pathways in Proteins
- SimTK Core 2.1 – Simbios Biosimulation ToolKit
- ISIM Interface 1.3.2 – Graphical Interface for running the program ISIM
- MALDSoft 1.0 – Admixture Mapping of Complex Trait Loci
- STRAT 1.1 – Companion program to Structure
- SelSim 2.1 – Simulate Population Genetic Data with Selection and Recombination
- Bayenv – Identify Loci Underlying Local Adaptation
- BFCounter 0.2 – K-mer Counting Software
- Transcriptome Assembler – Transcriptome Assembly used in RNA-seq of 16 Mammalian Species
- CENTIPEDE beta – Inference of TF Binding Sites
- Sfold 2.2 – Statistical Folding and Rational Design of Nucleic Acid
- C2A 1.0 – Coarse to Atomic
- NAST 1.0 – Nucleic Acid Simulation Tool
- PyOpenMM 3.0 – Python API of OpenMM Library
- SAFA 1.1 – Semi Automated Footprinting Analysis
- NAST-iEr 20110519 – Sequence Alignment Tool
- CAFA 0.41 – Capillary Automated Footprinting Analysis
- RNAG – Block Gibbs Sampler for RNA Prediction
- CONTRAST 1.0 – Multiple Sequence de novo Gene Predictor
- CONTRAfold 2.02 – RNA Secondary Structure Prediction
- CONTRAlign 2.01 – CONditional TRAining for Protein Sequence Alignment
- Bayes Aligner – Bayesian Adaptive Sequence Alignment Software
- BALSA – Bayesian Algorithm for Local Sequence Alignment
- Arlequin 3.5.1.3 – Population Genetics Data Analysis
- FBAT 2.0.4 – Family-Based Association Test
- WEASEL 3.0.2 – Flow Cytometry Data Analysis
- MarVis Suite 1.0 – Clustering & Visualization of Metabolomic Markers
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