2011 September
- Spotter 0.5 – Identify Region of Interest near Associated Variant
- KARMA 0.9 – Aligner for Mapping Shotgun Sequencer FASTQ Read
- tripleM 1.0 – Use Partition-Ligation strategy and EM Algorithm to Reconstruct Hplotypes in trios
- motifGPU 1.0 – GPU-computing Accelerate Motif Analysis
- MotifOrganizer 0.1 Beta – Cluster large sets of DNA sequence motifs to identify common patterns
- HPeak 2.1 – Define Genome-wide ChIP-enriched Peaks in Human Genome
- HMS 0.1 – Hybrid Motif Sampler
- FESTA 2.0 – Fragmented Exhaustive Search for TAgSNPs
- BEST 1.0 – Bayesian Expression Search Tool
- CRC 1.1 – Dirichlet Process Model-based Cluster
- CN3D 4.3 – 3D Molecular Structure Viewer
- CNVEM 0.710 – Infer Carrier Status of CNVs in Large Samples from SNP Genotyping Data
- CopyMap 0.813 – Localization of Copy Number Variation
- TreeLD 1.0.1 – Map Complex Trait Loci
- CoaCC 1.0.1 – Simulate Case-control Study using Coalescent Framework
- GSM 0.3 – Genotype-based Matching
- BestRepeat 1.0 – Variance Components Linkage Analysis with Repeated Measurements
- GENOME 0.2 – Rapid Coalescent-based Whole Genome Simulator
- mRNA by SNP Browser 1.0.1 – Graphical Overviews of Whole-genome Association Study
- SIBMED 1.0 – Identify Likely Genotyping Errors and Mutations
- RELPAIR 2.0.1 – Relationship of Pairs of Individuals based on Genetic Marker Data
- LocusZoom 1.1 – Visualization of Genome-wide Association Scan Result
- OFF-TARGET PIPELINE 1.5.4.2 -Identify Off-targets of Pharmaceuticals
- SMAP 2.0 – Comparison & Similarity Search of Protein Three-dimensional Motif
- QuickPDB 20021101 – Java Applet for quickly viewing PROTEIN PDB Structure
- Compare3D – Structure Alignment of Two or More Polypeptide Chains
- HDBStat 1.5 – Statistical Analysis of High Dimensional Biology Data
- GMDR 1.0 – Detect Gene-by-Gene and Gene-by-Environment Interactions
- BhGLM 1.0 – Bayesian hierarchical GLMs to Genetic Data Analysis
- SIMLINK 4.12 – Estimate the Power of a Proposed Linkage Study
- SIMLA 3.3 – SIMulation of Pedigree Data for Linkage and Association Studies
- SIBSIM 2.1.3 – Phenotype Simulation in Extended Pedigrees
- VisProt3DS 3.03 – Stereoscopic Visual Analyzer of Biological Macromolecules
- QuteMol 0.41 – Molecular Visualization System
- PDBlib 2.2 – C++ Macromolecular Class Library
- GDIS 0.90 – Visualization Program for Molecular and Periodic Systems
- Jimp 2 0.091 – Visualize and Manipulate Molecules
- SOOP 2.16 – System for Optimized Overgo Picking
- ROMPrev 0.2.1 beta – Revised Regression of Offspring on Mid-Parent
- GrASP 0.6 beta – Graphical Assessment of Sliding P-values
- GASP 3.31 – Genometric Analysis Simulation Program
- GeneLink 1.7 – Data Management System to Facilitate Genetic Studies of Complex Traits
- CDPred 1.01 – Conserved Domain-based Prediction
- SKIPPY 1.3 – Detection of Exonic Variants that Modulate Splicing
- Wildfire/GEL 2.0 – Build Workflows
- ClustalW-MPI 0.13 – ClustalW Analysis using Distributed and Parallel Computing
- CLICK – Comparison of Biomolecular 3D Structures
- DEPTH 2.8.7 – Measure Extent of Atom/Residue Burial within Protein
- BioPAX level 3 – Biological Pathway Exchange Language
- StrBio 1.2 – Java Classes for Computational Structural Biology
- ANDY 0.2 – Large Biological Database Searching on Computer Clusters
- SUBOPT – Aligns Two Protein Sequences
- Alphabet – Find Groups of Amino Acids that Co-occur in Columns Frequently
- eBLOCKS – Database of Conserved Protein Regions
- ALION 1.0 – Pairwise Sequence Alignment
- eSIGNAL 1.0 – Database of Medline MeSh Terms & Protein Motifs that Detect Signal Transduction Proteins
- CBA 200504 – Consistency Based Alignment
- FoldMiner 200312 – Structural Similarity Searches and Motif Discovery
- LOCK 2.0 – Vector-based Protein Structure Alignment
- eMATRIX 2.0 – Fast Probabilistic Analysis of Sequence Function using Scoring Matrices
- 3MATRIX 1.0 – Motif in 3D
- 3MOTIF 2.0 – Motif in 3D
- eBAS 3.6 – eMOTIF Batch Analysis Suite
- EMOTIF 3.6 – Sequence Analysis Using Pareto-optimal Discrete Motifs
- MotifRegressor – Find DNA Sequence Motifs
- CompareProspector – Sequence Motif Finding Algorithm
- xMAN 20060717 – MAp OligoNucleotides to Subject Genome
- MAT build 3 – Model-based Analysis of Tiling-arrays for ChIP-chip
- SageExpress 1.0 – Process SAGE-Seq High Throughput Gene Expression Data Set
- CEAS 1.0.2 – Cis-regulatory Element Annotation System
- NPS 1.3.2 – Nucleosome Positioning from Sequencing
- BINOCh 1.0.0 – Binding Inference from Nucleosome Occupancy Changes
- BioOptimizer 2.0 – Bayesian Scoring Function Approach to Motif Discovery
- BioProspector 2004 – Find Enriched Sequence Motifs
- MDScan 2004 – Find Motif from ChIP-on-chip Targets
- Gmaj 20081103 – Interactive Viewer for Multiple Sequence Alignments
- zPicture / multi-zPicture – Dynamic Alignment & Visualization Tool
- PipMaker/MultiPipMaker 20110812 – Alignments of Similar Regions in Sequences
- MOSAIC 201011 – ImageJ plugin for Biological Fluorescence Microscopy
- Darwin 2.1 – Programming Environment for Bioinformatics
- SIBsim4 0.20 – Align an Expressed DNA Sequence with a Genomic Sequence based Sim4
- MolTalk 3.0.1 – Computational Environment for Structural Bioinformatics
- ESTScan 3.03 – Detect Coding Regions in DNA/RNA Sequences
- PSORTb 3.0.3 – High-precision Localization Prediction for Bacterial Proteins
- Ortholuge 0.8 – Improve Specificity of High-throughput Ortholog Prediction
- ArrayPipe 1.7 – Processing & Analysis of Microarray Data
- ProbeLynx 1.2.2 – Update the Association of Microarray Probes to Genes
- MOBY 1.15 / BioMoby – Interoperability between Biological Data Hosts and Analytical Services
- SeqHound 3.02 – Bioinformatics Database Warehouse Resource
- TOADS – TOpologies in Alignments of DNA Sequences
- SIRENS – SImulating REcombination in Nucleotide Sequences
- BARCE 1.2 – Bayesian Application for Recombination and Gene Conversion Estimation
- TetraploidMap 1.0.6 – Calculate Linkage Maps for Autotetraploid Populations
- CurlyWhirly 1.10.12.10 – Multi-Dimensional Data Visualization
- PhyloGibbs-MP 2.0 – Motif Finder in Cis-regulatory Sequences of DNA
- Sigma 2.0 BETA – Non-coding DNA Sequence Alignment
- Famtypes 1.4 – Utility for Parsing PED files
- L-POP 1.2 – Analysis Model for Detecting Population Stratification
- gPLINK 2.050 – Graphical Interface for PLINK
- GEOMI 07 – Visual Analytic tool for Biological Networks
- PexSPAM 1.2 – Protein Sequence Feature Extraction
- BH – Markov Model for Phylogenetic Analysis
- SeqVis 1.5 – Visualization of Compositional Heterogeneity in Large Alignments of Nucleotides
- CARGO 2.0 – Web Portal to Integrate Biological Information
- Elements 2.3.1 – Elegant Periodic Table
- Viewmol 2.4.1 – Molecule Viewer
- Tessellator 1.0 – Software for Tessellation of 3D Volume in Biological Molecule
- SeqQR 1.0.1 – Generate Nonredundant set of Protein Tree
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