DNA / Genome Analysis
- BIC-seq 2.1.1 – Copy Number analysis from Whole-genome Sequencing data
- Tea 0.6.2 – Transposable Element Analyzer
- Reprever – Find and Reconstruct Extra Copies given Copy Number Gain Regions
- Wessim 1.0 – Whole Exome Sequencing SIMulator using in silico exome capture
- Sibelia 2.1.2 – aka Synteny Block ExpLoration tool
- AcE 0.5 – A System for Analyzing the Accuracy of Gene Prediction Programs
- project – Projects Genomic Features onto their Sequences
- overlap – Compute Overlap between two sets of Genomic Features
- MitoCounter 1.0.1 – Counting mitochondrial DNA Reads from Whole Genome Sequence
- SeqEntropy 2.0.1 – Assessmemt tool of Sequence Repeats for Short Read Sequencing
- HnaTyping 20120804 – HNA Genotyping From WGS
- Savant 2.0.3 – Sequence Annotation Visualization & Analysis Tool
- IGB 7.0.2 – Visualization for Genome-scale Data
- Genome Workbench 2.7.5 – View & Analyze Sequence Data
- ASD – Admixture of Dictionaries Analysis of the Regulatory Genome
- DISCOVER – Model for Factor Binding site Discovery in Metazoan Genomes
- CSMET – Multispecies Supervised Motif Finder
- read2SNPs 2.0.5.6 – Compare Set of NGS raw Short Reads for finding SNPs
- KisSplice 1.8.1 – Local Transcriptome Assembler for SNPs and AS events
- PhyloCSF 20121028 – Distinguish Protein-coding and Non-coding Regions
- STARFISH 2 – Identify Rigid Components with the Pebble Game and a Body-bar-and-hinge Reduction
- GiRaF 1.0.2 – Find Reassortments in Collections of Influenza Genome Sequences
- Jellyfish 1.1.10 – Counting of K-mers in DNA
- Tabusearch – DNA Sequencing by Hybridization with Isothermic Libraries
- PyroBayes 0.9 – Base Caller for SNP Discovery in Pyrosequences
- FreeBayes 0.9.6 – Bayesian Genetic Variant Detector
- BAMTOOLS 2.2.3 – C++ API and Toolkit for Analyzing and Managing BAM files
- MuSi – Analysis of Gene Libraries Generated by Dodon-directed Mutagenesis
- AUGUSTUS 2.7 – Gene Prediction for Eukaryotes
- GAMP 0.1 – GLOBAL ANALYSIS OF METHYLATION PROFILES
- MIM – Motif Independent Metric
- N-score – Predict Nucleosome Positions from DNA Sequence information
- TCW 1.0 – Transcriptome Computational Workbench
- Artemis 15.0.6 – Genome Browser and Annotation Tool
- CAIAP – Codon Adaptation Index Analyser Package
- Unique – Find Sequences that are repeated once or a precise number of times in DNA
- DNA Fragmentator – Restriction Analysis of DNA Templates
- SNUFER – Localization and Presentation of SNP
- DNA Baser 3.5.4 – DNA Sequence Assembly & Analysis
- WebSat 1.1.0 – MicroSatellite Marker Development
- UPIC 1.2 – Perl scripts to determine the number of SSR markers to run
- Kraken 13-100 – Tools for Quality Control and Analysis of High-throughput Sequence data
- RepeatMasker 4.0.1 – Screen DNA Sequences for Interspersed Repeats and Low Complexity DNA Sequences
- MeDiChI 0.4.0 – Model-Based ChIP-chip Deconvolution Algorithm
- GenPlay v584 – Genome Analyzer and Browser
- Repeatoire – ab inito Prediction of Repeat Families
- growthpred 1.07 – Prediction of Growth-related Traits in Microbes from Genomic and Metagenomic data
- Morpheus 2.0 – Prediction of Transcription Factors Binding Sites based on Position Weight Matrix
- DRIMust – Discovering Ranked Imbalanced Motifs using suffix trees
- RepWords 1.1 – Detect Tandem Repeats in FASTA Sequences
- PCI 1.0 – Calculate Barcode Gap Probability of Correct Identification of Species.
- GLOBAL 1.0 – Statistical Significance of Semi-global Block Alignments
- FLANK 1.0 – Calculate Statistical Parameters governing Over-extension of biologically related Alignments into surrounding random sequences.
- FASTA Unscramble Record Order 1.0 – Sorts one FASTA file according to the deflines of Another
- FASTA Unique Sequences 1.0 – Uniques the Sequences in a FASTA file
- FASTA Match Regular Expression 1.0 – Selects FASTA records whose deflines match a Perl Regular Expression
- FASTA Length 1.0 – Finds the Lengths of Sequences in a FASTA file
- FASTA Composition 1.0 – Find Overall Composition of Sequence
- Possum – Detect Cis-elements in DNA Sequences
- THetA 0.02 – Tumor Heterogeneity Analysis
- PREGO 1.0 -Paired-End Reconstruction of Genome Organization
- IMEx 2.0 – Imperfect Microsatellite Extractor
- NmerFreq – Compute the Frequency of N-mers of that size in the Genome
- BioWord 20120923 – Sequence Manipulation Suite for Microsoft Word
- scNCA – Obtain Self-consistent Reference Set using NCA (or CAI) Codon Bias Index
- RCA – Relative Codon Adaptation index
- FiToM 1.0 / xFITOM 1.03 / jFITOM 1.0 – Detection of Binding Sites in DNA or RNA Sequences
- Sequence Analysis 1.7.2 – Bioinformatics Consultant
- DiScRIBinATE – Distance Score Ratio for Improved Binning and Taxonomic Estimation
- ProViDE – Program for Viral Diversity Estimation
- ValFold 1.0.0 – Program for the Aptamer Truncation Process
- Precise – Predict Regulatory Cis-acting Elements
- IGIPT – Integrated Genomic Island Prediction Tool
- GenoViewer 0.9.0 – Viewer/Browser for the Sam/Bam format
- UNIPOP 0.1 – UNIversal Predictor of OPerons
- OperonDT 0.1 – Operon Predictor using Decision Tree Approach
- Psafe – Pooled Sequencing Allele Frequency Estimation
- EGID 1.0 – Improved Genomic Island Detection in Genomic Sequences
- BEST 1.0.1 – Binding-site Estimation Suite of Tools
- GIST 1.0 – Predicting Genomic Islands in Genomic Sequences
- Marina 1.01 – Identification of Over/under-represented TFBSs given large sets of Promoter-sequences
- SRA Software Toolkit 2.3.1 – Sequence Read Archive Software Toolkit
- AFLPinSilico v2 – Simulating AFLP Fingerprints
- VISCOE 1.0 – Visual Integration Software for Conditional Omics Experiments
- VESPA 1.1.1 – Visual Analytics Platform for Exploring Proteogenomics data
- YPA 1.6 – Repository of Promoter features in Saccharomyces cerevisiae
- TFBSs 1.0 – Predict Transcription Factor Binding Sites
- RDNAanalyzer – Secondary Structure Pprediction and Analyzing DNA
- Multifasta Analysis 0.1 – Get Informations about a set of Contigs
- Quality Filter – Filter Sequences based on Phred Quality
- Quality Assessment 0.5 – Analyse the Quality of the Next-generation Reads
- Simplifier 0.4 – Eliminate Redundant NGS Contigs
- Sequence Maneuverer – Sequence Extraction from Genomes
- MethFinder – Tissue specific SVM based Methylation Prediction tool
- FOOTER 2.0 – Find Ammalian Transcription Factor Binding Sites using Phylogenetic Footprinting
- enoLOGOS 1.0 – Web tool for Energy Normalized Sequence Logos
- G-InforBIO 1.90 – E-Workbench for Comparative Genome Analysis
- OCW – Identify Over-represented and Conserved Words
- PMSearch – Poly Matrix Search
- RASTA-Bacteria – Rapid Automated Scan for Toxins and Antitoxins in Bacteria
- AutoGRAPH – Web Server for Automating and Visualizing Comparative Genome Maps
- DSK 1.49 – K-mer Counting software
- ViralFusionSeq 20121207 – Discover Viral Integration Events and Fusion Transcripts
- gKaKs 1.2.2 – Genome level calculate Ka/Ks
- Decombinator – Tool for Analysing T cell Receptor Sequences
- RetroSeq 1.34 – Transposable Element Discovery from Next-generation sequencing data
- Readscan 0.5 – Pathogen Discovery program with accurate genome relative abundance estimation.
- ChromoZoom – web-based Genome Browser
- Scribl 1.1.4 – HTML5 Canvas Genomics Graphic Library
- Musket 1.0.6 – Parallel and Scalable Multistage K-mer Spectrum based Error Corrector for Illumina Sequence data
- ANACONDA 2.0 – Study of Genes’ Primary Structure
- PIntron 1.2.57 – Gene-structure Prediction based on Spliced Alignments of Transcript Sequences.
- BamReadCount 0.01 – Calculate Read Count for each region in the input list of Regions
- QPLOT 20120602 – Quality Assessment and Diagnosis tool for Sequencing
- NGSUtils 0.5.0c – Tools for Next-generation Sequencing Analysis
- BioScript – Python Library of Bioinformatics Scripts
- HTSstation beta – High-throughput Sequencing Data Analysis portal
- BroadPeak – Broad Peak calling algorithm for Diffuse ChIP-seq Datasets
- CG-Pipeline 0.3.2.1 – Computational Genomics Pipeline
- MGIP – Meningococcus Genome Informatics Platform
- CTMCStateSeq 1.0 – State Sequence Analysis
- MaSC – Mappability-Sensitive Cross-Correlation
- AKDESeq – Adaptive-bandwidth Kernel Density Estimation for High-throughput Sequencing data
- CLaMS / iClaMS – Classifier for Metagenomic Sequences
- Hammer 0.2 – Error-correction of High-throughput Sequencing Datasets
- SilVA 1.0.1 – Silent Variant Analysis using random Forests
- Encore 1.2 – Polymorphism-friendly Error Correction
- Dalliance – Interactive Genome Viewing on the web
- amrfinder 1.02 – Detect Allelle-specific DNA Methylation
- PRINSEQ 0.20.2 – Preprocess and Generate Statistics about Sequence data
- Atlas-Link 0.01 – Link Genome Sequence Contigs into Scaffold
- Atlas2 1.4.3 / Atlas2Cloud 0.5 – Genome Analysis Suite
- Faster2 0.22 – Extensible Tool for working with FASTA and FASTQ files
- SCOPE++ 0.31 – Sequence Classification Of homoPolymer Emissions
- ZMap 0.13.0 – Feature Annotation Viewer
- eXpress 1.3.0 – Streaming Quantification for High-throughput Sequencing
- libStatGen 1.0.8 – C++ Library for Handling and Analyzing Next Generation Sequencing and Genotyping Data
- SeqMonk 0.24.0 – Visualisation and Analysis of Mapped Sequence Data
- GenomeTools 1.5.0 – Genome Analysis Software
- bamUTIL 1.0.7 – Perform Operations on SAM/BAM files
- Picard 1.85 – Manipulate SAM files
- VarScan 2.3.4 – Variant Caller for Short Sequence Reads
- ASAP 1.1.7 – Automated Sequence data Processing on Computer Clusters
- MotifSuite 201302 – Probabilistic Motif Detection
- MAK 1.94 – Automated MITE analysis
- JBrowse 1.8.1 – JavaScript Genome Browser
- ACT 12.0.0 – Display Pairwise Comparisons between DNA Sequences
- Chromas Lite 2.1 / Chromas 2.4 / ChromasPro 1.74 – Sequence & Chromatogram Editor
- InVEx – Ascertain Genes with a Somatic Mutation Distribution showing evidence of Positive Selection for non-silent Mutations
- GATK 2.3-9 – Analysis Tools for Next-generation DNA Sequencers
- MEME 4.9.0 – Discovering Motifs within the Sequences
- Apollo 1.11.8 – Genome Annotation Viewer & Editor
- PSTk-Classifier – Classify DNA using a Bayesian approach
- MegaDot 0.9 – Large Scale Dot Plotter
- BCM Trace Viewer – Display .scf Traces and Phred Quality values
- Attacca 0.27 – Annotator for Bacterial DNA
- CAMBerVis 1.5 – Visualization of Comparative Analysis of multiple Bacterial Strains
- CAMBer 2 – Comparative Analysis of Multiple Bacterial Strains
- CompleteMOTIFs – Motif Discovery Platform
- Dawg 1.2 – Simulating Sequence Evolution
- SeqMap 2.0 – Identify Viral Integration Sites
- Exome Power Calculator – Analysis of Exome Sequencing
- ModuleMaster 1.1 – Identify Cis-regulatory Modules using Promoter Analysis and Microarray Expression data Regression
- bbq – Discovering Dis-regulatory modules
- BEBaC 20130114 – Estimate Bacterial Community Composition from 454 Sequencing data
- GAT 0.1 – Genome Annotation Test with Validation on Transcription Start Site and ChIP-Seq for Pol-II Binding Data
- tfbs_species 1.0 – Map Human Transcription Factor Binding Sites to Another Species
- absee 1.0 – Reads ABIF files
- ProStar – Structural Parameters for Promoter Prediction
- PIPAx 2.1.2 – Bioinformatics Analysis and Management of NGS data
- Masai 0.6 – Fast and Sensitive Read Mapping
- FusionMap 20121208 – Detecting Fusion Genes from Next-generation Sequencing data at Base-pair Resolution
- Paraclu 9 – Find Clusters in Data attached to Sequences
- PCS 1.5 – Identify and Analyze Conserved K-mers in Pairwise Alignment
- Triplet-SVM – Predict a query sequence with Hairpin Structure as a real miRNA precursor or not
- methylKit 0.5.6 – R package for DNA methylation analysis
- QualSim 0.4 – Quality Score Simulator for Next-gen Sequencer Output
- PipeMeta Beta 0.44 – Run a de novo Transcriptome Annotation Pipeline
- FinchTV 1.5 – Trace Viewer
- SNPHunter 1.75 – dbSNP Search & Management
- MaCS 0.5b – Markovian Coalescent Simulator
- Goby 2.1.2 – Next-generation Sequencing Data Management
- ChIPMunk 4.1 – DNA Motif Digger
- NextGenMap 0.4.3 – Map NGS Reads against a Reference Genome
- USeq 8.5.0 – Analyze Next Generation Sequencing data from Illumina, SOLiD, and 454 platforms
- ShotGun 1.0.10 – Flexible Short Read Simulator
- MetaPhyler 1.25 – Taxonomic Profiling for Metagenomic Sequences
- Circoletto 20121015 – Visualize Sequence Similarity with Circos
- Sherman 0.1.3 – Bisulfite-treated Read FastQ Simulator
- Bismark 0.7.7 – Aligner and Methylation Caller for Bisulfite-Seq Applications
- mrCaNaVaR 0.41 – Micro-read Copy Number Variant Regions
- AceDB 4.9.60 – Genome Database System
- mseq 1.2 – Modeling non-uniformity in Short-read Rates in RNA-Seq data
- npSeq 1.1.1 – Significance Analysis of Sequencing data
- PoissonSeq 1.1.2 – Significance Analysis of Sequencing data based on a Poisson log linear model
- Metarep 1.4.0 – High-performance Comparative Metagenomics Tool
- inGAP 2.8.2 – Integrated Next-gen Genome Analysis Platform
- GenomeView 2020 – Next-generation Genome Browser and Editor
- GBrowse 2.54 – Genome Viewer
- GeneWall Genome Browser 1.2 – Genome Browser for the iPad/iPhone
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