2011 November
- SplitDist 1.1.7 – Calculate Number of Splits (edges) that Differs for two Trees
- QuickJoin 1.0.10 – Fast Canonical Neighbor-joining Tree Construction
- QDist 2.0.2 – Computation of Quartet Distance between Evolutationary Trees
- HapCluster 2.2.0 – Software Package for Association Mapping
- GeneRecon 1.2.1 – Coalescent based Tool for Fine-scale Association Mapping
- CoaSim 4.2.0 – Simulating Coalescent Process
- CoAnnealing 0.1 – Simulated Annealing Search for Coalescent Trees
- Blossoc 1.4.0 – Whole-genome Association Mapping tool
- RecPars – Parsimony Analysis of DNA Sequences
- SEQL 2.0 – Sequence Learner
- ELL 3.2.2 – Platform for Generic Algorithms
- BIU 2.3.6 – Bioinformatic Utility Library
- MEMERIS 1.0 – MEME in Rna’s Including Secondary Structures
- MARNA 100729 – Server for Multiple Alignment of RNAs
- LocalFold 1.0 – Local Folding of RNA
- INFO-RNA 2.1.2 – A Server for Inverse Folding of RNA
- IntaRNA 1.2.5 – RNA-RNA Interaction Prediction
- LatPack 1.9.0 – Folding Studies for Arbitrary Lattice Protein Models
- probA 0.1.1 – Stochastic Pairwise Sequence Alignments
- TARGETING 1.0 – Solver for the Maximal Pairing Problem on Arbitrary Trees
- RNAsoup 1.0a – Structural Clustering Pipeline for Structured RNAs
- RNAstrand 2.0.0 – Predict Reading Direction of Structured RNAs in Multiple Sequence Alignments
- pwmatch 0.1 – Recognizing Position Weight Matrix hits in a sequence
- PLEXY – Target Pprediction for Box C/D snoRNAs
- RNAsnoop 0.2 – Target Prediction for H/ACA snoRNAs
- RNAxs – Design Potent siRNAs
- RNAplex 0.2 – Search for Short Interactions between two long RNAs
- noisy 1.5.12 – Identify Homo-plastic Characters in Multiple Sequence Alignments
- NetwPartLearn 0.0.1 – Simulation Tool for Reverse Engineering of Genetic Networks
- NcDNAlign 1.0.7 – Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences
- Kinwalker – Algorithm for Prediction of RNA Folding Trajectories
- HelixPSO – Particle Swarm Optimizer for RNA Secondary Structure Prediction
- GotohScan 2.0 – Gene finding via Semi-global Alignment
- galculator 1.0 – Nucleotide frequency counter
- FRANz 2.0 – Reconstruction of Pedigrees
- fragrep 2 – Efficient Search for Fragmented Patterns in Genomic Sequences.
- cyclope 0.1 – Multiple circular DNA Sequence Alignments
- Tracker 2.0 – Footprint Detection and Alignment Consistency Determination
- creto 1.0 – Determination of Cis-Regulatory Element Turn-Over rates
- codaln 1.0 / code2aln 1.2 – Progressive Multiple Alignments of Partially Coding Sequences.
- blockbuster – Detect Blocks of Overlapping Reads
- bbq – Discovering Cis-regulatory Modules
- aln3nn 0.6.0 – Multiple Alignment tool based on Alignment of Sequence Triplets
- RNAz 2.1 – Predict Structural Noncoding RNAs
- RNAdbtool – Update and Cleanup of Structural RNA Databases
- FOLDALIGN 2.1.1 / FOLDALIGNM 1.0.1 – RNA Structure and Sequence Alignment
- deepBlockAlign 1.0 – Align RNA-seq Profiles of Read Block Patterns.
- clasp 1.1 – Local Fragment Chainer using Sum-of-pair Gap Costs
- MaxAlike 1.0 – Phylogenetic Reconstruction of incomplete Sequences by Maximum Likelihood
- PETfold 2.0pre / PETcofold 3.1.2 – Folding of Multiple Alignment of RNA sequences
- SARSE 1.37 – RNA Sequence Editor
- RSAT 2011 – Regulatory Sequence Analysis Tools
- BioGUI 0.2 – GUI for highly used Bioinformatics Tools
- MPprimer 1.4 – Reliable Multiplex PCR Primer Design
- MFEprimer 2.0 – PCR Primer Specificity Checking Program
- CPC 0.9r2 – Assess Protein-coding Potential of Transcripts
- DART 0.2 – Library includes a number of Bioinformatics Alignment Programs
- ConStruct 3.2.5 – RNA Alignment Editor and Consensus Structure Prediction Tool
- EI_EXCHANGE 1.0 – Calculate Elementary Mode
- SEPARATOR – Decompose Large Biochemical Networks into Smaller Subsystems
- METATOOL 5.1 – Biochemical Reaction Networks Elementary Modes Analysis
- CBCAnalyzer 1.1 beta – Inferring Phylogenies based on Compensatory Base Changes
- GEPAT – Genome Expression Pathway Analysis Tool
- CHARMM 36 – Macromolecular Dynamics and Mechanics
- SPF 1.1 – Find Structurally Significant Regions in RNA Sequences
- Mc-Sym 3.3.2 – Molecular Modeling using Constraint Satisfaction
- RSMatch 2.0 – Align RNA Secondary Structures and Motif Detection
- HotKnots 2.0 – Predict Secondary Structures of RNA with or without Pseudoknots
- AveRNA – Ensemble-based Prediction of RNA Secondary Structures.
- MultiRNAFold 2.0 – Secondary Structure Prediction of RNA/DNA
- SOKOS/CAN 20070522 – Sequence Oriented Kernels over SCFG with Genome Scanning Capability
- BPLA kernel 1.0 – Structural RNA Analysis
- OSfinder 1.4 – Orthologous Segment Finder
- Murasaki 1.68.6 – Find Anchors from Multiple Genomes
- Rchange – Compute Energy Changes of RNA Secondary Structures
- Rentropy – Compute Entropy of RNA Secondary Structures
- Fdur – Compute Sufficient Statistics of Phylogenetic Tree Models
- Raccess – Genome-scale Computation of Structural Accessibility of RNA Transcripts
- SCARNA_LM 2.2 – Local Multiple Aligner for RNA Sequences
- miRRim 0.1 – Detect miRNA Foldbacks based on Hidden Markov Model
- CentroidAlign 1.0 – Aligner for multiple RNA Sequences
- CentroidFold 0.0.9 – Predict RNA Secondary Structure from RNA Sequence
- Stem Kernels 2.96a – Directed acyclic graph kernels for structural RNA analysis
- Rfold 0.1.1 – Compute local base pairing Probabilities
- PSTAG 2.1.4a – Model Pseudoknot RNA Structure
- PHMMTS 20070918 – Aligns Sequence to Sequence of Known Secondary Structure
- RNAmine – Extract Structural Motifs from a set of RNA sequences
- Murlet 0.0.1 – Practical Alignment tool for Structural RNA Sequences
- MXSCARNA 2.1 – Structural Multiple Alignment for long RNA Sequences
- OligoWalk 2 – Select Efficient siRNA using Hybridization Thermodynamics
- NUPACK – Analysis and Design of Nucleic Acid Systems
- Kinefold – RNA/DNA Folding Predictions
- jViz.Rna 2.0 – Visual Comparison of RNA Secondary Structure
- PSCE 1.01 – Pairwise Sequence Comparison / Evaluation
- doublet 1.0 – Incorporate Patterns of Dipeptide Covariation to Align Protein Sequences
- SIFTER 2.0 – Genome-scale Phylogenetic Function Annotation of Protein Families
- SeqLogo – Create Sequence Logo from RNA alignment file
- RZParser – Parse Ribose Zipper from PDB file(s)
- BioQuali 2 – Cytoscape Plugin for Analysing the Global Consistency of Regulatory Networks
- pdb2cif 2.4.2 – Cnvert from PDB format to mmCIF
- cif2pdb 2.0.3 – Convert mmCIF to Pseudo-PDB Format
- BioMyn – Mining Gene and Protein Knowledge
- BiLayout 1.0 – Cytoscape plugin for Analysis & Visualization of Molecular Interaction Networks
- ParaSAM – Parallel Version of the SAM Algorithm
- GENOM 2005 3.42 – Affymetrix Microarray Analysis
- topGO 0.97 – Calculat Significance of Biological Terms from Gene Expression Data
- STRuster 3.1 – Comparison and Analysis of Alternative Structural Models
- Mtreemix 1.3.00 – Learn & Use Mixture Models of Mutagenetic Trees
- MethMarker 1.0.678 – Facilitate Design of DNA Methylation Assays
- IRECS 1.3 – Predict Conformation of Protein Side Chains
- GOTaxExplorer 1.0 – Tool for Querying GOTaxDB
- Galinter 1.6 – Compare Protein-protein Interfaces
- DomainGraph 3.01 – Cytoscape Plugin of Analysis and Visualization of Molecular Interaction Networks
- CgiHunter 1.0 – Exhaustive CpG Island Annotation
- CalSpec 1.3 – Calculate Spectra
- K2N – Service to Get from Knotted to Nested RNA Structures
- SPuNC – RNA Structure Prediction using Nucleotide Composition
- FluxEs 2.0 – Metabolic Flux Estimation
- ALISS 1.2 – Alignment of Structures and Sequences
- FuLinkA 0.5 – Fuzzy Linking Assembler for Genomic Sequences
- RW 1.0 – Protein Structure Modeling and Structure Decoy Recognition
- HAAD – Quick and Accurate Hydrogen Atom Addition
- SPICKER 20101229 – Cluster Protein Structures for Near-native Model Selection
- MVP/MVP-Fit 2.0 – Macromolecular Visualization and Processing
- EDTSurf – Quick and Accurate Construction of Macromolecular Surfaces
- NW-align – Protein Sequence-sequence Alignments
- MM-align 20090930 – Protein Complex Structural Alignment
- BSpred – Predict Binding Site of Proteins
- SVMSEQ 1.0 – Protein Contact Prediction
- REMO 1.0 – Construct Full-atom Protein Models from C-alpha Traces
- ModRefiner 20111024 – High-resolution Protein Structure Refinement
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