2011 December
- Isofinder – Isochore Computational Prediction
- Html4blast 1.7a – Text to HTML Blast Results Formatter
- GenoProfiler 2.1 – Process Fingerprinting Data
- geneid 1.4.4 – Predict Genes in Anonymous Genomic Sequences
- Framedp 1.20 – Sensitive Peptide Detection on Noisy Matured Sequences
- FPC 9.4 – Build Contigs from Fingerprinted Clones
- Enredo 0.5 – Produce Colinear Segments from Extant Genomes
- Repbase Submitter 1.1.115 – Format & Annotate Repbase Entries
- Treecon-Tools 0.1 – Convert Phylogenetic Trees File Formate
- SpliceMachine – Splice Site Prediction Tool
- Randfold 2.0 – RNA Minimum Free Energy of Folding Randomization Test
- ProSOM 2.5 – Promoter Prediction Program
- pppbenchmark 1.3 – Promoter Prediction Programs
- Pathicular 1.55 – Cytoscape plug-in of Identifies Path Motifs
- MatrixClust 20080804 – Fuzzy Clustering of a Symmetric Matrix
- i-ADHoRe 3.0 – Detect Degenerated Genomic Homology
- HyperGeny – View Large Phylogenetic Trees
- GaneSh – Cluster Expression Data by Gibbs sampling procedure
- FunSiP 0.8.1b – Prediction of Functional Sites in DNA
- EP3 1.10 – Promoter Prediction Program
- DASS-GUI 1.4 – Pattern Search in Non-sequential Data
- CyClus3D 3.3 – Cytoscape plugin for Identifying Functional Modules
- ASaturA – Discriminate Amino Acid Substitutions
- ADHoRe – Detect Genomic Regions
- Hydra 0.5.3 – Structural Variation Discovery with Paired-end-mapping
- UbPred – Determine whether a Lysine Residue in a protein is ubiquitinate
- FANN-GO – Predict Gene Ontology terms for a given protein sequence
- Graphlet kernel 1.01 – Annotate Functional Residues in Protein Structures
- Composition Profiler 1.1 – Discovery of Amino Acid Composition Differences
- Two Sample Logo 1.21 – Calculate Differences between two sets of Aligned Amino Acids or Nucleotides
- MSOAR 2.0 / MultiMSOAR 2.0 – Ortholog Assignment on Genome Scale.
- LRTag – Select SNP Markers across Multiple Populations
- MSTMap – Construct Genetic Linkage Maps
- MergeMap – Construct Accurate Consensus Genetic Map
- Overgo Maker 4.0 – Output Overgo Sequences ready for ordering from a fasta input file
- FASTAParse 0.0.3 – Parsing Module for handling FASTA formatted sequence
- EXOR 0.02 – Filters Mutually Exclusive Alignment Events
- MagicViewer 1.2.1 – Integrated Solution for Next-generation Sequencing Data Visualization
- SSAHA 2.5.5 – Sequence Search & Alignment by Hashing Algorithm
- MIRO 2.9 – Analyze microRNAs using Next-generation Sequencing Data
- MapView 3.4.1 – Visualization of Short Reads Alignment
- Maqview 0.2.5 – Graphical Read Alignment Viewer
- Maq 0.7.1 – Mapping and Assembly with Qualities
- BFAST 0.7.0 – Alignment Tool for Large Scale Genome Resequencing
- NIP_NSc – Dentify Compactness at Protein-protein Contacts
- Seg2Dgel 0.5.12 – 2D Electrophoresis Gel Spot Segmenter
- PrediSi – Predict Signal Peptide Sequences
- JVirGel 2.2.3 – Create Virtual 2D Pretein Gel
- Open2Dprot 20060607 – Proteomics Exploratory Data Analysis Software
- Flicker 0.87.2 – Compare 2D Gel Images
- PrestoPlot 1.23 – 2D Plotting tool
- Fragmentation - Fragmentation of the Gel Image into Sections
- TopSpot 3.0 – Analysis of the Gel Image
- TipDate 1.2 – Estimate the rate of Molecular Evolution
- GoCore 5.0.1 – Protein Sequence Alignment and Analysis
- AiO 8 – Integrate Oligo ordering/Data Base and DNA/Protein programs
- GeSTer – Dentify Terminators in Bacterial Genome Sequences
- Staden 2.0.0b9 – DNA Sequence Assembly , Editing and Analysis
- Ridom TraceEdit 1.1.0 – Free DNA Trace Editor
- SPLITS 1.1 / SPLITSX – tRNA Detection in Genome Sequence
- cDNA Analysis Package 0.1.0 – Analysis of Annotated cDNAs
- Restauro-G 1.0 – Genome Re-Annotation System for Comparative Genomics
- G-language 1.8.13 – Genome Analysis Environment
- Ori-Finder 1.0 – Find OriCs in Unannotated Bacterial Genomes
- GC-Profile 2.0 – Visualize and Analyze Variation of GC Content in Genomic Sequences.
- ZCURVE 1.0 / ZCURVE_CoV 1.0 / ZCURVE_V 1.0 – Recognize Protein Coding Genes in Genomes
- Gene Designer 2.0 – Design of Synthetic DNA Segments
- LIQUID 1.0 – Pymol Plugin for Fuzzy Pharmacophore Models
- MyRAST r44 – Annotate Genome
- PAL2NAL v14 – Conversion of Protein Sequence Alignments into Corresponding Codon Alignments
- AQUA 1.1 – Automatic Quality Improvment for Multiple Sequence Alignment
- Medusa 3.0 – Visualization and Clustering Analysis of Biological Network
- FANMOD 20061223 – Fast Network Motif Detection.
- NAViGaTOR 2.2.1 – Visualize and Analyze Protein-protein Interaction Networks.
- CASP 1.2.3beta1 – Image Analysis of Comet Assay
- LutefiskXP 1.0.7 / Lutefisk – De novo Interpretation of Peptide CID Cpectra
- MS-Clustering 20110327 – Clustering Millions of Tandem Mass Spectra
- Cycloquest 20110907 – Identification of Cyclopeptides via Database Search
- CSPS 2.0.0 – Comparative Shotgun Protein Sequencing
- ArrayOligoSelector 3.8.4 – Design Gene Specific Long Oligonucleotide Probes
- SOAP 3 – Short Oligonucleotide Analysis Package
- MUMmer 3.23 – Alignment of Large-scale DNA & Protein Sequences
- OliCheck – Test Validity of Potential Microarray Probes
- PASTAA – Detecting Transcriptions Factors Associated with Functional Categories
- TRAP 3.04 – Transcription factor Affinity Prediction
- qcalculator 1.0 – Calculate Relative mRNA Gene Expression
- QGene 4.3.10 – Software for QTL data exploration
- qPCR-DAMS 1.2 – Analyze, Manage, and Store Quantitative Real-Time PCR data.
- MOSBY 0.955 – View Atomic Structures of Protein Molecules
- GUPPY 0.988 – Visualize Sequence Annotation Data
- ALNGG – Exon Finding by Genomic Sequence Comparison
- PRRN 3.5.2 – Multiple Sequence Alignment by Doubly Nested Randomized Iterative Method
- ALN 3.5.2 – Pairwise Alignment of Biological Sequences Supporting Spliced Alignment Procedures
- PerlPrimer 1.1.21 – Open-source PCR Primer Design
- NormFinder 0.953 – Normalization of Real-Time Quantitative Reverse Transcription-PCR Data
- Genevestigator V3 – Gene Expression Search Engine
- DART-PCR 1.0 – Quantitative Real-time PCR Data Analysis
- GenEx 5.3.6 – Analyze Real-time qPCR Data
- OligoCalc 3.19 – Oligonucleotide Properties Calculator
- MACSIMS 1.42 – Multiple Alignment of Complete Sequences Information Management System
- Dotlet 1.5 – Comparing Sequences by Diagonal Plot Method
- H-BloX 1.47N – Visualizing Alignment Block Entropies
- ESPript 2.3 – Generate Pretty PostScript Output from Aligned Sequences
- AMOS 3.1.0 – Whole Genome Shotgun Assembler
- XMatchView 0.2 – Visualize DNA Sequence Alignments.
- TreeBuilder3D 1.0 – Interactive Viewer for Gene Expression Data
- THOR 1.0 – Assemble Target Genomic Sequence Orthologs
- SSAKE 3.8 – Assembling Millions of short DNA Sequences
- SAM 1.0 – Sequence Assembly Manager
- Novel miRNA detection 1.0 – Identification of novel miRNA genes
- LaneRuler 1.1 – Identify Lanes in Gel Image
- VancouverShortR 4.0.16 – Vancouver Short Read Analysis Package
- FASSI 1.0 – Fingerprint and ASSembly Incorporation
- DiscoverySpace 4.0 – Interactive Data Analysis Application
- SliderII 1.1 – High Quality SNP Calling Using Illumina Data at Shallow Coverage
- MiRNA Profiling 0.2.6 – Profile Content of miRNA Sequencing Run.
- CoNAn-SNV 0.11.9 – Discovery of Single Nucleotide Variants in WGSS data
- SNVMix 0.11.8 – Detect Single Nucleotide Variants from Next Generation Sequencing
- BLISS 0.7 – Identify Batch Effects in RNA Expression Data
- Anchor 0.3.1 – Post-processing Tools for de novo Assemblies
- PASsiT 1.0 – Post Alignment SNV Tools
- GEPIS – Gene Expression Profiling in silico
- Bluejay 1.3 – Mining Genome-Scale Data
- VADAR 1.8 – Structural Analysis of Protein Coordinates
- xalign 6.1 – Multiple Sequence Alignment
- Orb 1.2 / orbplus 1.1.2 – Chemical Shift Prediction
- GSC 1.2 – NMR Chemical Shift Comparison
- SimCell 1.8.0b – DCA Cell simulator
- RCI – Predict Protein Flexibility by Calculating Random Coil Index
- GelScape 20030728 – Web-based Gel Viewing and Annotation System
- Genquire 3.4.1 /WinGenquire 1.1 – Genome Annotation Workstation
- Sockeye 1.3 – 3D Visualization for Working with Genomic Information
- Chinook 1.2.2 – Peer-to-peer (P2P) Bioinformatics Service
- OSCAR 6.1.1 – Open Source Cluster Application Resources
- GOtcha 200812 – Prediction of Gene Function by Application of Gene Ontology
- NoD 1.3 – Nucleolar Localization Sequences Detection
- Haplotype meta-analysis – Meta-analysis of Haplotype Association Studies
- Poisson meta-analysis – Mixed-Effects Poisson Regression Models for Meta-Analysis
- metatrend – Estimate Trends in Cumulative Meta-analysis
- GeneViTo – Genome Visualization Tool
- metagen – Meta-analysis of Genetic association Studies
- Consensus v6c1 – Web Interface for Finding DNA and Protein Patterns
- Diametrical Clustering – Identify Anti-correlated Gene Clusters
- Probalign 1.4 – Multiple Sequence Alignment
- GAME – Utilize Genetic Algorithm to Find Motifs
- MiSink 1.01 – Cytoscape Plugin for Database of Interacting Proteins
- JCat 1.0 – Java Codon Adaptation Tool
- GenMAPP2.1 / GenMAPP-CS 0.2 – GenMAPP Pathway Analysis and Visualization in Cytoscape
- RSpredict – Predict Secondary Structures of multiple RNA Sequence Alignments
- RSfold – Predict Secondary Structures of Single RNA Sequence
- UpdownDistance – Tool for comparing phylogenetic trees
- TMatch – compute Editing Distance of Two Ordered Trees
- Sdiscover – Tool for Finding Motifs in Sequences
- RADAR 2.0 – RNA Data Analysis and Research
- Erpin 5.5.4 – RNA Motif Search program
- HIERFSTAT 0.04-6 – Package for R to Compute & Test Hierarchical F-statistics
- Twinscan/N-SCAN 4.1.2 – Gene Structure Prediction
- Validate GTF 1.0 – Check GTF file for Correctness
- PPFINDER 1.0 – Find Processed Pseudogenes in Genome Annotations
- primerD 1.0 – Design of Unique Degenerate Primer Pairs
- Pairagon 1.1 – Pair-HMM based cDNA-to-genome Alignment
- Trace Recalling 0.5 – Deconvolute Double Traces Resulted from Simultaneously Sequencing Two DNA Templates
- iParameterEstimation 0.3.1 – Maximum Likelihood Parameter Estimation Package
- eval 2.2.8 – Analysis of Genome Annotations
- GRENDEL 0.2 – Gene Regulatory Network Decoding Evaluations tooL
- N-Sieve 0.1 – Network Inference tool that uses an attenuation based structural prior
- GrailEXP 6.2 – Grail Experimental Gene Discovery Suite
- MISO 1.0 – RNA-Seq Experiments for Identifying Isoform Regulation
- Darn 1.0 – Non-protein-coding RNA Detection
- FrameD 20070223 – Predict Coding Regions in Prokaryotic and Eukaryotic Sequence
- BAGEL 4.1.1 – Bayesian Analysis of Gene Expression Levels
- MJOIN 1.2 – Neighbor Joining with Subtree Weights
- Mercator 2010.10.11 – Multiple Whole-Genome Orthology Map Construction
- Distance 1.0 – Estimation of Reversible Substitution Matrices and Evolutionary Distance
- RIND 6.9.4 – Reconstructed Independence
- Weighbor 1.2 – Weighted Neighbor Joining
- ARTS – Alignment of RNA Tertiary Structures
- Parasight 7.6 – Visualize and Analyze Biological Pairwise Alignments
- COSEG 0.2.1 – Identifies Repeat Subfamilies
- comrad 0.1.3 – Discovery of Gene Fusions using Paired End RNA-Seq and WGSS
- SPLITREAD 0.1 – Split read based INDEL/SV Caller
- ProKware 0.95 – Present Protein Structural Properties in Protein Tertiary Structures
- iGEMDOCK 2.1 – Recognizing Pharmacological Interactions and Virtual Screening
- parredHMMlib 1.0 – Library for Hardware Accelerated HMM Parallelizing Analysis
- HMMlib 1.0.2 – Library for Hardware Accelerated HMM analysis
- SMA 1.2.1 – Single Marker Association Tests
- SNPFile 2.0.1 – Library and API for Association mapping and Population Genetics
- DrawTree 0.1.3 – Translate Newick format into Graphical Formats
- Newick 1.3 – Python Parser for the Newick Tree Format
- Benchware® 3D Explorer 2.7 – 3D Chemical Visualization
- Chemitorium 4.0 – Molecule Editor & 3D Chemical Structure Viewer
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