Posts
- Category: DNA / Genome Analysis (continued)
- QuGAcomp 0.99.1 - R package for Quantitative Comparison of Differential ChIP-seq data
- Quikr 1.0.4 - Rapid Reconstruction (Phylotyping) of Bacterial Communities
- QuorUM 1.1.1 - Error Corrector for Illumina Reads
- QVZ / QVZ2 0.1 - A Lossy Compressor for Quality Scores in Genomic Data
- R'MES 3.1.0 - Finding Exceptional Motifs in Sequences
- R2R 0.950 - Analysis of Short Read Sequence data obtained by NextGen Sequencing Techniques
- R453Plus1Toolbox 1.42.0 - Importing and Analyzing data from Roche's Genome Sequencer System
- Rabema 1.1 - Read Mappers
- RACER 1.0.1 - Rapid and Accurate Correction of Errors in Reads
- RADAR v0.2.4 - Differential Methylation analysis for m6A Sequence data
- RADplex - RADSeq Demultiplexing tool
- RADtools 1.2.4 - Software for Restriction site Associated DNA Sequencing
- RALP 1.11 - Calculation of the Gumbel Parameters for Repeats
- RAMACO - Compute Rare Maximal Exact Matches between Multiple Sequences
- RAMBO-K 1.21 - Read Assignment Method Based On K-mers
- RAMMCAP 20130510 - Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline
- RANDNA - Random DNA Sequence Generator
- RASTA-Bacteria - Rapid Automated Scan for Toxins and Antitoxins in Bacteria
- RASTtk 1.3.0 - Rapid Annotation using Subsystem Technology tool kit
- RAT 1.0 - Recombination Analysis Tool for High Throughput Analysis of Genomic Sequence
- RATT r18 - Rapid Annotation Transfer Tool
- RazerS 3.5.8 - Fast Read Mapping with Sensitivity Control
- RCA - Relative Codon Adaptation index
- RCandy 1.0.0 - Visualising Homologous Recombinations in Bacterial Genomes
- RCircos 1.2.1 - R package for Circos 2D track plots
- RDNAanalyzer - Secondary Structure Pprediction and Analyzing DNA
- RDXplorer 3.2 - CNVs Detection in Whole Human Genome Sequence data
- ReadDepth 0.9.8.4 - Detects Copy Number Aberrations in Deep Sequencing Data
- Readscan 0.5 - Pathogen Discovery program with accurate genome relative abundance estimation.
- ReadSim 0.12 - Simulator for Sanger and 454 Sequencing
- ReadSim 1.6 - Read Simulator for Long Reads
- ReadXplorer 2.2.3 - Visualization and Analysis of Mapped Sequences
- REannotate - Automated Molecular Paleontology of Complex DNA Repeats
- Reaper 17-257 - Demultiplexing, Trimming and Filtering Short Read Sequencing data
- Recco 0.93 - Recombination Analysis Using Cost Optimization
- RECKONER 0.2.1 - Read Error Corrector Based on KMC
- ReCo RoKo - Reverse Complement by Robert Kofler
- RECON 1.05 - Identification of Repeat Families from Genomic Sequences
- RecoverY - Classification of Y-chromosome Specific Reads
- RecPars - Parsimony Analysis of DNA Sequences
- Recycler v0.7 - Detecting Plasmids from de novo Assembly Graphs
- Redeem 1.1 – Detect Sequencing Errors in Illumina reads
- REDseq 1.36.0 - Analysis of High-throughput Sequencing data processed by Restriction Enzyme Digestion
- REEF - Search REgionally Enriched Features in Genomes
- Refcomp 4.x - Compare Reference Sequence with Consensus Sequence
- RefCov 0.3 - Analyzing Coverage of Sequence data across a Reference
- Refgenie v0.12.1 / refgenieserver v0.7.0 - Reference Genome Resource Manager
- Refget v0.1.0 - Refget Sequence Identification and Retrieval
- regshape v1.1 - DNA Shape-based Classifier for Regulatory Elements(R pkg)
- ReMixT v0.5.18 - Clone-specific Genomic Structure Estimation in Cancer
- REMOCOD - REgulatory MOtif COmbination Detector
- repDNA 1.1.4 - Generate various modes of Feature Vectors for DNA Sequences
- Repeat Enrichment Estimator - Measure Enrichment of Annotated Repeat Types in ChIP-seq data
- RepeatAround 2.1 - Find Repeats in Circular Genomes
- RepeatExplorer2 0.3.8 - Repeat Discovery and Characterization using Graph based Sequence Clustering
- RepeatFinder - Finding Repetitive Sequences Complete and Draft Genomes
- RepeatHMM v2.0.3 - Estimation of Repeat Counts on Microsatellites from long-read sequencing data
- RepeatMasker 4.1.0 - Screen DNA Sequences for Interspersed Repeats and Low Complexity DNA Sequences
- RepeatModeler 2.0.1 - de-novo Repeat Family Identification and Modeling package
- RepeatRunner - Repeat Identification and Masking in Dipterans
- RepeatScout 1.0.5 - Discover Repetitive Substrings in DNA
- RepeatSeq v0.8.2 - Genotyping Microsatellite Repeats Tool
- REPET 3.0 / PASTEClassifier 2.0 - Detection, Annotation and Analysis of Repeats in Genomic Sequences
- REPFIND 20040309 - Find Clustered, Exact Repeats in Nucleotide Sequences
- REPK 1.3 - Restriction Enzyme Picker
- Reprever 0.1.1 - Find and Reconstruct Extra Copies given Copy Number Gain Regions
- Reptile 1.1 – Short Read Error Correction
- Reputer - Compute and Visualize Repeat Structures
- RepWords 1.1 - Detect Tandem Repeats in FASTA Sequences
- ResampleSeq - Sequence Resampler
- RESCRIPt 2021.8.0 - REference Sequence annotation and CuRatIon Pipeline
- RescueNet 0.91 - Codon usage Anaysis and Gene Prediction
- Restauro-G 1.0 - Genome Re-Annotation System for Comparative Genomics
- RetroMap 0.021 - Characterize LTR Retroelements on a Genome Scale
- RetroPred - Prediction, Classification and Extraction of non-LTR Retrotransposons
- RetroSeq 1.41 - Transposable Element Discovery from Next-generation sequencing data
- ReverseComplement 1.8 - Reverse Complement of DNA and RNA sequences
- ReviSeq 0.1.2 - Revising Bacterial Genome Sequences
- Rgb 1.6.1 - Genome Browser for R
- RHOM - Research of HOMogeneous regions in DNA sequences
- Riboswitch Scanner - pHMM based application for Detecting Riboswitches from Genomic Sequences
- Rice Gene Thresher 2.0 - Mining Genes underlying QTL in Rice Genome
- Ridom TraceEdit 1.1.0 - Free DNA Trace Editor
- RIPCAL 2.0 - Analysis of RIP in Fungal Genomic DNA Repeats
- RISCI – Repeat Induced Sequence Change Identifier
- RISO - Motif Discovery Tool
- RISOTTO - Motif Discovery Tool
- RITA 1.0.1 - Rapid Identification of Taxonomic Assignments for Metagenomic fragments
- RLM - Read level DNA methylation analysis of Bisulfite Converted Sequencing data
- RnBeads 2.10.0 - Comprehensive DNA Methylation Analysis
- RNF / RNFtools 0.3.1.3 - general Framework to Evaluate NGS Read Mappers
- RNIE 0.01 - Predicting Rho Independent Terminators in Bacterial Genomes
- Roary 3.13.0 - Prokaryote Pan Genome Analysis
- RopeBWT2 r187 - Incremental construction of FM-index for DNA sequences
- ROVER 20050711 - Find Relatively Overrepresented Motifs in DNA Sequences
- RPAN 0.91 - Rice Pan-genome Browser for 3K rice genomes
- RPMCMC 0.2 - Repulsive Parallel MCMC Algorithm
- RQS 0.1.0 - Read Quality Sparsifier
- RRS - Comparison of regulatory DNA Sequences
- rSW-seq - Detection of Copy Number Alterations in Deep Sequencing data
- RTanalyzer - Searche for Retro-transposition Elements in the Human Genome
- RTMg - Real Time Metagenomics
- rtracklayer 1.52.0 - R interface to Genome Browsers and their Annotation Tracks
- Ruby UCSC API 0.6.5 - An API for the UCSC Genome Database
- rush 1.4 - Recombination detection Using SHustrings
- RVD - Rare Single Nucleotide Variant Detection using Next-generation Sequencing
- RVD 27 - Hierarchical Bayesian model to detect Rare Single Nucleotide Variants
- rVista 2.0 - Identification of TFBS Conserved in Pairwise Alignments
- S-Peaker - Single-Peak Transcription Start Sites finder
- SA-SSR - A Novel Algorithm for SSR Discovery in Genetic Sequences
- SAAP-BS 1.0 - Streamlined Analysis and Annotation Pipeline for RRBS
- SADMAMA 20110410 - Motif Scanning and Detection of Significant Variation
- SAGExplore - Map SAGE tags against Genomic Annotation
- SAIC - Identify Significant Consensus Aberrations in Cancer Genome
- SALT 20140716 - Protein Domain Classifier
- Sambamba 0.8.0 - Tools for working with SAM/BAM data
- Samscope 1.6.6.91 - Lightweight SAM/BAM File Viewer
- SAMStat 1.5.1 - Display Sequence Statistics for Next Generation Sequencing
- SAP 1.9.6.1 - Statistical Assignmnet Package
- Sarek 2.7.1 - Detect Germline or Somatic Variants from Whole Genome or Targeted Sequencing
- Sarment 5 - HMM Sequence Partitioning and Maximal Predictive Partitioning
- SatFind - C-program for Finding Satellites in Genomes
- SBARS - Spectral-Based Approach for Repeats Search
- SBT / SSBT 0.1 - (Split) Sequence Bloom Tree
- SCA - Sequence Composition Analysis
- ScaffMatch 0.9 - Scaffolding Algorirthm Based on Maximum Weight Matching
- Scaffold-filling - Software for Filling the Scaffold
- SCALCE 2.8 - Sequence Compression Algorithms using Locally Consistent Encoding
- Scalpel 0.5.4 - Genetic Variants Discovery tool
- Scimm 0.3.0 - Sequence Clustering with Interpolated Markov Models
- Scipio 1.4.1 - Ukaryotic Gene Identification
- SciRoKo 3.4 / SciRoKoCo - Whole Genome Microsatellite Search and Investigation / SSR-search module.
- scNCA - Obtain Self-consistent Reference Set using NCA (or CAI) Codon Bias Index
- SCONE 0.61 - Sequence CONservation Evaluation
- SCOPE 2.1.0 - Suite for Computational identification Of Promoter Elements
- SCOPE++ 20130523 - Sequence Classification Of homoPolymer Emissions
- SCRAP ++ v1 - Sequence Cleaning and Removal of Adapter Sequences using Profile HMMs
- Scribl 1.1.4 - HTML5 Canvas Genomics Graphic Library
- scrm 1.7.4 - Coalescent Simulator for Biological Sequences
- Scurgen - Exploring Genomic data with Space-filling Curves
- SCYN - Single Cell CNV profiling method using Dynamic Programming
- SDDA - Stochastic Dictionary-based Data Augmentation for Sequence Motif Discovery
- Sdiscover - Tool for Finding Motifs in Sequences
- SDT v1.2 - Sequence Demarcation Tool
- SeAMotE - Sequence Analysis of Motifs Enrichment
- SEAN - SNP Prediction and Display Programs
- SearchRepeats - Detection of Exact Repeats by a Compression Algorithm
- SEAStAR v0.5.0 - Analysis of Next-generation Metagenomes
- SeCaPr v1.1.15 - SEquence CApture PRocessor
- secureSeq - Secure Sequencing Analysis Tools
- SEDA 1.4.0 - SEquence DAtaset builder
- SeDD 20141028 - Sequence Diversity Diagram
- SeedMasker - Genome Masking based on High Occurrence Words
- sefOri 1.0 - Selecting the best engineered sequence features to predict DNA Replication Origins
- segemehl 0.3 - Fast Short Read Mapping with Indels
- SEGID - Conserved Segment Identification
- Segment 1.04 - Identifying Compositional Domains in DNA Sequences
- Segminator II 0.1.1 - Analysis of viral data generated using the 454 Life Sciences Sequencing Platform
- SegSeq 1.01 - Detect CNVs from Short Sequence Reads
- Segtools 1.2.4 - Provide Exploratory data Analysis on Genomic Segmentations
- Segtor 1.3 - Annotation of Genomic Coordinates and Single Nucleotide Variations using Segment Trees
- Segway 3.0.3 - a way to Segment the Genome
- SEK - Bacterial Community Composition
- Selene 0.4.8 - Library for deep-learning-based Sequence models
- Selenoprofiles 3.6 - Profile-based Scanning of Eukaryotic Genome Sequences for Selenoprotein Genes
- selscan 1.3.0 - EHH-based Scans for Positive Selection
- SEME 1.0 - A de novo Motif Finder for ChIP-seq data
- SEND - Compute the Standard Errors of Nucleotide Diversity and Nucleotide Divergence
- SENDBS - Computes Average Nucleotide Substitutions within and between Populations
- Seq2Hosts - Predict Hosts of Coronaviruses
- SeqAnt - Sequence Annotator
- SeqBench 1.0 - Integrated Solution for the Management and Analysis of Exome Sequencing data
- SeqClean 20110222 - Trim & Validation of ESTs or other DNA sequences
- SeqCorator 2.03 - Sequence Editor & Feature Decorator
- SeqEntropy 2.0.1 - Assessmemt tool of Sequence Repeats for Short Read Sequencing
- SEQERR - Estimates Genotype Error Rates for Whole-genome Sequence data
- SeqGrapheR 0.5.2.4 - Graph based Visualization of Cluster of DNA sequence reads
- SEQIO 1.2.2 - Read and Write Biological Sequence Files
- seqjoin - Predict Complete cDNA Insert Sequence
- SEQL 2.0 - Sequence Learner
- SeqMap 1.0.13 - Map Millions of Short Sequences to Genome
- seqMINER 1.3.3e - Genome Wide Mapping data Interpretation Platform for NGS(ChIPSeq)
- SeqMonk 1.48.0 - Visualisation and Analysis of Mapped Sequence Data
- SeqMule 1.2.6 - Automated Pipeline for Variant Calling from FASTQ files
- Seqool 3.1 - Search Biological Signals in Nucleic Acid Sequences
- Seqpare v1.0.0 - Novel Metric of Similarity between Genomic Interval Sets
- SeqPup 0.9 - Biosequence Editor
- seqRFLP 1.0.1 - Predicting RFLP from DNA sequences
- SeqServe 0.1 - Management of Sequencing Samples
- SeqStrap 1.0 - Extrapolating Partial or Fragmentary Nucleic Acid Sequences prior to Assay Design
- SeqToolBox 0.02 - A set of Perl modules and scripts for Operations on Sequence data
- SeqTrace 0.9.0 - Rapidly Processing DNA Sequencing Chromatograms
- SeqTrimMap 1.0 - Sequential Trimming and Mapping of Short Reads
- Sequedex 2.1.1 - Classifies DNA Sequences by Analyzing Collections of Sequences
- Sequence Analysis 2020 - Bioinformatics Consultant
- Sequence Extractor 1.1 - Generates Restriction Map and PCR Primer Map
- Sequence Maneuverer - Sequence Extraction from Genomes
- Sequence Scanner 1.0 - View, Edit, Print and Export sequence data
- Sequence Searcher - Search Sequences for Specified Sequence Motifs
- SequenceJuxtaposer 1.2 - Browse and Compare Gene Sequences
- Sequescence 1.0 - Simulates the Appearance of Miscoding Lesions
- sequtils 0.2.9 -software for Sequence Manipulation
- SeqWord /OligoWords 1.2.1 - Oligonucleotide usage of all Sequenced Bacteria from the NCBI RefSeq collection
- SeqyClean 1.10.09 - Next Generation Sequencing Cleaning
- SERIAL CLONER 2.6.1 - DNA Cloning, Sequence Analysis & Visualisation
- Serial NetEvolve 1.0 - A flexible utility for generating serially-sampled Sequences along a Tree or Recombinant Network
- SESAME 1.0 - Analyze Amplicon Sequences obtained through NGS Technologies
- SeSiMCMC 4.36 - Dig For DNA Motifs Gibbs Sampler
- SEWAL 20100804 - Next Generation DNA Sequencing Analysis and Visualization
- SGI - Detect Positive and Negative Selection at Individual Codon Sites
- sgp2 1.1 - Predict Genes by comparing Anonymous Genomic Sequences from two different Species
- ShatterSeek v0.5 - Identification of Chromothripsis Events from Whole-genome Sequencing data
- SHEAR 1.1.2 - Sample Heterogeneity Estimation and Assembly by Reference
- Sherman 0.1.8 - Bisulfite-treated Read FastQ Simulator
- Shimmer 0.2 - Detection of genetic Alterations in Tumors using Next-generation Sequence data
- SHM 0.1 - Models of Somatic Hypermutation
- SHORE 0.9.3 - Analysis Suite for Illumina Short Read Data
- SHOREmap 3.6 - Mutant Mapping with Next Generation Sequencing data
- ShortCAKE - Shortest sequence to Cover All K-mErs
- ShortRead 1.42.0 - Classes and Methods for High-throughput Short-read Sequencing data
- ShotGun 1.0.10 - Flexible Short Read Simulator
- ShotgunFunctionalizeR 1.2-9 - Functional Comparison of Metagenomes
- ShotMap - Shotgun Metagenome Annotation Pipeline
- SHOW 20111109 - Structured HOMogeneities Watcher
- SHREC 2.2 - Short Read Error Correction
- shulen 1.0 - Null Distribution of Shortest Unique Substring Lengths
- shustring 2.6 - Compute SHortest Unique SubSTRINGs
- Sibelia 3.0.7 - Synteny Block ExpLoration tool
- Sickle 1.33 - Windowed Adaptive Trimming for Fastq files using Quality
- SigHunt - Horizontal Gene Transfer Finder optimized for Eukaryotic Genomes
- SIGMA 1.0.2 - Strain-level Identification of Genomes from Metagenomic Analysis for Biosurveillance
- SigmaPromoter 1.0 - Promoter Prediction method based on multiple Sigma Factors model for Bacterial Genomes
- sigMatch - Fast and Scalable Multi-Pattern Matching
- SilVA 1.1.1 - Silent Variant Analysis using random Forests
- SimAncestry 1.0 - Extract Archaic introgressed sequences from ms Simulation Output
- SimiTri 1.1 - Visualise Similarity Relationships for Groups of Sequences
- simLoci 1.0 - Simulate Sequence data on an input Topology
- simMSG - Simulate Accuracy of MSG for your Genome
- simNGS 20130502 - Simulate Observations from Illumina NGS machines
- SIMPLEX 2.0 - Cloud-enabled pipeline for the comprehensive analysis of Exome Sequencing data
- Simplifier 0.4 - Eliminate Redundant NGS Contigs
- SimPlot 3.5.1 - Sequence Similarity Plotting
- simuG v1.0.0 - General-purpose Genome Simulator
- SIOMICS 3.0 - Systematic Identification Of Motifs In ChIP-Seq data
- Sircah 1.0 - Detection and Visualization of Alternative Transcripts
- SIRENS - SImulating REcombination in Nucleotide Sequences
- Siscan - Detect Recombination
- SISSRs 1.4 - Genome-wide Identification of in vivo Protein-DNA Interactions from ChIP-Seq data
- SiteFind 4.0 - A Site-directed Mutagenesis Software Tool
- SITES 1.1 - Analysis of Comparative DNA Sequence data
- SiteSampler 1.1 - Sample Sites of Sequence Alignment to Produce Replicate Data Sets
- Skewer 0.2.2 - Adapter Trimmer for Next-generation Sequencing Paired-end Reads
- SKIPPY 1.3 - Detection of Exonic Variants that Modulate Splicing
- SKraken - Classification of Short Metagenomic Reads based on filtering uninformative k-mers
- SliderII 1.1 - High Quality SNP Calling Using Illumina Data at Shallow Coverage
- SLR 1.4.3 - Sitewise Likehood Ratio Estimation of Selection
- Sma3s - Sequence Massive Annotation
- SMaRTFinder DR4 - Search Biosequences for Structured Motifs
- SmashCommunity 1.6p2 - Metagenomic Analysis and Annotation Tool
- SMETHILLIUM 1.2 - Spatial normalisation METHod for ILLumina InfinIUM HumanMethylation BeadChip
- SMRT Analysis 2.3.0 - Software Suite for Sequence Alignment, Assembly, Variant Detection, and Base Modification discovery
- SMRT View 2.3.0 - Genome Browser that visualizes data generated by PacBio® Sequencing System
- SMUG - Somatic Mutation Gleaner for Detecting Tumor Somatic Mutations
- SnackVar v2.4.3 - Sanger Sequencing analysis in Clinical Environment
- SNAP 1.1.1 - Synonymous/Non-synonymous Analysis Program
- SNAP 20131129 - Gene Prediction tool.
- Snippy 4.6.0 - Find SNPs/indels in a Bacterial Genome from NGS reads
- SnowyOwl 2.1.0 - RNA-Seq based Gene Prediction pipeline for Fungal Genomes
- SNP-o-matic 1.0 - Stringent Short-read Mapping software
- SNP-VISTA 1.0 - SNP Visualization tool
- SNPGenie - Estimating Evolutionary parameters to Detect Natural Selection using pooled NGS data
- SNPHunter 1.75 - dbSNP Search & Management
- SnpStore 1.0 - SNP and Indel Calling in mapped NGS Sequencing Reads
- SNPSVM - A Support Vector Machine for Calling Variants from Next-gen Sequencing data
- SNPtrack - Mutation Mapping and Identifying causal Mutations from Whole-genome Sequencing Studies
- SNVer 0.5.3 / SNVerGUI - Rare and Common Variants Detection in Next Generation Sequencing
- SNVMix2 - Detect Single Nucleotide Variants from Next Generation Sequencing
- SoftSearch 1.0 - Structural Variant (SV) Detection tool
- Sole-Search v2 - Peak Detection and Functional Annotation using ChIP-seq data
- SolexaQA 3.1.7.1 - Quality Assessment of Illumina Second-generation Sequencing data
- SoloDel 1.0.0 - Somatic Low-frequent Deletion Caller Model
- SomatiCA 1.12.0 - Analysis of Somatic CNAs from Cancer Genome Sequencing
- SomaticCall 46233 - Find Substitutions between Sequence Data
- SomaticSeq 3.3.0 - Accurately Detect Somatic Mutations
- SomaticSniper 1.0.5 – Somatic SNV Detection for Whole Genome Resequencing Data.
- SOMBRERO 1.1 - Motif Finder
- SOPanG v2.0.0 - Online Text Searching over a Pan-genome
- Spaced Words - Alignment-free Sequence Comparison
- SPANDx 3.2 - Comparative Analysis of Haploid Next-generation Re-sequencing data
- SparkSeq - Interactive Genomic data analysis with Nucleotide Precision
- specI 1.0 - Species Identification tool
- SpeedSeq v0.1.2 - Framework for Rapid Genome Analysis and Interpretation
- SPInDel 1.2 - Species Identification by Multiplex Analysis of Variable-length Sequences
- Spines 1.15 - C++ Software Package for Genomic Sequence Alignment and Analysis
- SplazerS 1.1 - Detect Genomic Indel Variants with exact Breakpoints in Single- and Paired-end Sequencing
- SPLICEATOR 2.1 - Multi-species Splice Site prediction program using Convolutional Neural Networks
- SpliceMachine - Splice Site Prediction Tool
- SplicePie - Pipeline to Analyze Non-sequential and Multi-step Splicing
- Splicing Express - Alternative Splicing Analysis using Next-generation Sequencing data
- SpliCQ 1.0 - Predict Alternative Splicing Events in Next Generation Sequencing data
- SPLINTER - Identification of Indel Variants in Pooled DNA with Spike-in Controls
- SplitMEM 1.0 - Graphical Pan-genome Analysis with Suffix Skips
- splitMixed - Finding in a matched Tumor/normal paired-end reads dataset a consistent explanation
- SPLITREAD 0.1 - Split read based INDEL/SV Caller
- SPMM - Estimating Infection Duration of Multi-variant HIV-1 Infections
- SpolPred - Predict the Spoligotype from raw Sequence reads
- Sprites 0.3.0 - Deletion Finder through re-aligning the Whole Soft-clipping Read
- SQPR 8.01 - Sequence Quality Plate Reader
- SRA Software Toolkit 2.11.0 - Sequence Read Archive Software Toolkit
- SRCP 1.0 - Sequence Read Classification Pipeline
- SRF 1.1 - Find Repeats through an analysis of the power Spectrum of a given DNA Sequence
- Srfim 0.0-95 - Short-Read Filtering and Intensity-Modeling
- SRinversion - Detection of Short Inversions in Human Genome using Next Generation Sequencing Data
- SRST 2-0.2.0 - Short Read Sequence Typing for Bacterial Pathogens
- SRTOOLS - Python Library for Short Read Analysis.
- SSEdit 6.08 - Single (Short) Sequence Editor
- SSpred - Splice Site Prediction with Regulatory Elements and Dependencies
- STAMP 1.1 - Microsatellite Marker Design Extension for the Staden package
- STAMP 1.1 - Tool-kit for DNA Motif Comparison
- STAMP 2.1.3 - Analyze Metagenomic Profiles
- STAN 2.20.0 - STrand-specific ANnotation of Genomic data
- STAP v2 - Sequence To Affinity Prediction
- STAR - Search for Tandem Approximate Repeats
- STARFISH 2 - Identify Rigid Components with the Pebble Game and a Body-bar-and-hinge Reduction
- STEME 1.9.6 - Motif Finder for large data sets
- stepwise 0.3 - Stepwise Detection of Recombination Breakpoints
- SToRM 0.0099 - Seed-based Read Mapping tool for SOLiD or Illumina sequencing data
- Straglr v1.1.1 - Short-tandem Repeat Genotyping using long Reads
- stringMLST - An ultrafast k-mer based MLST tool
- Strmat - String Matching and Pattern Discovery
- StructRED - Structural Cis-Regulatory Element Detector
- STS 1.4 - Suffix Tree Searcher
- Stubb 2.1 - Finding Cis-regulatory Modules
- Subread 2.0.2 / RSubread 2.6.1 - Processing Next-gen Sequencing data
- subSeq 1.20.0 - Determining Appropriate Sequencing Depth through Efficient Read Subsampling
- Suite16 2.1 - Co-localizes and Displays Genomic Features
- SULDEX 0.01 - Simultaneous Ultra high throughput Ligand Dissociation EXperiment
- Sunflower 1.1.0 - Model for Natural Selection in Promoters
- SUPER-FOCUS 0.34 - Agile Functional Analysis of Shotgun Metagenomic data
- Sushi 1.30.0 - Tools for Visualizing Genomics Data
- SV-Bay - Detection of Structural Variants in Cancer Mate-pair and Paired-end data
- SVA 1.10 - Sequence Variant Analyzer
- SVGen v1 - Simulation of Structural Variants in Next-generation Sequencing data
- SVGenes 0.4.1 -SVG Format Genome Browser Style Pictures
- SVMerge 1.2r37 - SVs Analysis by Integrating Calls from several existing SV callers
- SVMotif 0.1 - A SVM Based Transcription Factor Binding Motif Finder
- SVseq 2.2 - Detecting exact Breakpoints of Deletions with Low-coverage Sequence data
- svviz 1.5.2 - A Read Viewer for Validating Structural Variants
- Swan v6 - Motif Scanning
- SWAP454 46233 - Call SNPs using 454 Read Data
- SwDMR 1.0.7 - Differentially Methylated Regions Identification and Annotation
- Swift - Primary data analysis for Next-gen DNA Sequencers
- SWIFT 1.0.1 / BALSAM 1.3 - Fast Local Alignment Searching
- SWITCHdna - SupWald Identification of dna-copy Changes
- Sybil 1.5.1 - Web-based software for Comparative Genomics
- SyMAP v5.0.6 - Detect Syntenic Relationships
- Syn-SCAN 0.9 - Synonymous Nonsynonymous Mutation Rates between Sequences Containing Ambiguous Nucleotides
- SynoR - Genome Scanner for Gene Regulatory Elements with Synonymous Function
- Synteny - Investigate Sequence Conservation between Species
- T-lex 2.2.2 - Assessment of Transposable Element Presence in Next-generation Sequencing data
- T-REKS - Identification of Tandem Repeats
- Tabusearch - DNA Sequencing by Hybridization with Isothermic Libraries
- TAEC - an R package for Taxonomic Analysis by Elimination and Correction
- TagCleaner 0.16 - Detect and Remove Tag Sequences from Metagenomic datasets
- TAGCNA 1.0 - Identify Significant Consensus Events from Copy Number Alterations in Cancer Genome
- TagDust 2.33 - Extracts Mappable Reads from NGS gata.
- Tagger 1.3 - Genome/Transcriptome-wide Tag Scanner
- TAGOOS 0.2.1 - Associated Tag SNP Boosting
- Tail-tools 1.8 - 3'-seq Analysis Toolset
- TakeABreak 1.1.2 - Detect Inversion Breakpoints directly from raw NGS reads
- TALENoffer - Genome-wide TALEN Off-target Prediction
- TALgetter - Predicting TAL Effector Target Sites
- TAMER 1.0 - Taxonomic Assignment of Metagenomic Sequencing Reads
- TAMO 20120321 - Analyze Transcriptional Regulation using DNA-sequence Motifs
- TandemSWAN - Divergent Tandem Repeats Searching
- TANGO 1.2.0 - Taxonomic Assignment in Metagenomics
- Target Explorer - Identification of new Target Genes for a specified set of Transcription Factors
- targetSeqView - Visualize Next Generation Sequencing Reads over Putative Structural Variants
- TASUKE ver.20201117 - Visualization program for Large-scale Resequencing data
- TCGA2STAT 1.2 - Simple TCGA Data Access for Integrated Statistical Analysis in R
- TCW 3.2.5 - Transcriptome Computational Workbench
- TD 2.0 - Computation of the Transformation Distance for a set of DNA sequences
- Tea 0.6.2 - Transposable Element Analyzer
- TEclass 2.1.3C - Classification of TE Consensus Sequences
- Teiresias 0.9.1 - Combinatorial Pattern Discovery in Biological Sequences
- TESS 1.0 - Predict Transcription Factor Binding Sites in DNA sequence
- TFBIND - Searching Transcription Factor Binding Sites
- TFBS 0.7.1 - Perl modules for Transcription Factor Binding Site Detection and Analysis
- TFBS Scanner - Scanning for Transcription Factor Binding Sites
- TFBSs 1.0 - Predict Transcription Factor Binding Sites
- TFBSTools 1.30.0 - Transcription Factor Binding Site (TFBS) Analysis
- TFM-Explorer 2.0 - Analysing Regulatory Regions in Eukaryotic Genomes
- TFM-Scan - Efficient Location of Position Weight Matrices on a DNA sequence
- TfReg 5.3- Calculating DNA or RNA Melting Temperatures and Average Strand Openings
- TGAC Browser 0.2.0 - Web-based Genomics Browser
- THetA 0.7 - Tumor Heterogeneity Analysis
- ThioFinder 1.2 - Identification of Thiopeptide Gene Clusters in DNA sequences
- Tiara 1.0.2 – a tool for DNA sequence Classification
- TinT - Screening for Nested Transpositions from Genome Assemblies or Trace data
- TIPR - Transcription Initiation Pattern Recognition on a Genome Scale
- Tn-seq Explorer 1.5B - Analysis of High-throughput Sequencing data of Transposon Mutant Libraries
- TOADS - TOpologies in Alignments of DNA Sequences
- TomeTools 1.03 - Tools to work with large NGS datasets
- TOUCAN 3.1.1 - Regulatory Sequence Analysis on Metazoan Genomes
- Trace Recalling 0.5 - Deconvolute Double Traces Resulted from Simultaneously Sequencing Two DNA Templates
- TRACE-RRBS v0.1 - Targeted Alignment and Artificial Cytosine Elimination for RRBS
- trace2dbEST 3.0.1 - Turn Traces into Expressed Sequence Tags
- trace2seq 1.0.1 - Process Capillary Sequencing Traces
- TraceView 2.01 - Java Applet for viewing Sequence Traces
- tracy v0.5.9 - Basecalling, Alignment, Assembly and Deconvolution of Sanger Chromatogram trace files
- TransGeneScan 1.3.0 - Gene Finding tool for Metatranscriptomic Sequences
- TRANSIT 3.2.1 - Analysis of Tn-Seq data
- TRANSPO - Searching for Transposons with known TIR
- Transposome 0.12.1 - Annotation of Transposable Element Families from Unassembled Sequence Reads
- TransTermHP 2.09 - Transcription Terminator Predictions
- TRAP 1.1 - Tandem Repeats Analysis Program
- TRAP 3.05 - Transcription factor Affinity Prediction
- TREAT 1.0.1 - Targeted RE-sequencing Annotation Tool
- Trebol 20111212 - Interactive Comparative Genomics Tool
- TreeGibbsSampler - Identifying Conserved Motifs without Aligning Orthologous Sequences
- TreQ 0.1 beta - Indel-tolerant Read mapping
- TreqCG 0.3 - Clustering Accelerates High-Throughput Sequencing Read Mapping
- TRF 4.09 - Tandem Repeats Finder
- TRhist 1.0.1 - Tandem Repeat Profiler in Personal Genomes
- TriageTools 0.2.2 - Partitioning and Prioritizing Fastq data
- trieFinder - Annotating Digital Gene Expression (DGE) Tags
- Trimmomatic 0.39 - A Flexible Read Trimming tool for Illumina NGS data
- Triplet-SVM - Predict a query sequence with Hairpin Structure as a real miRNA precursor or not
- Triplex-Inspector 0.1.3 - Triplex Target Analysis Toolkit
- Triplexator 1.3.2 - Finding Nucleic Acid Triple Helices
- TRIplot 1.0.1 - Finds Direct and Inverse Repeats by Comparing a Sequence to itself
- TriTISA - Prediction of Translation Initiation Site for Microbial Genomes
- Trowel 0.2.0.4 - Error Correction Module for Illumina Sequencing Reads
- TRTools v4.0.0 - Toolkit for Genome-wide analysis of Tandem Repeats
- TS4MSBH - Tabu search algorithm for DNA Sequencing by Hybridization problem
- TSDfinder - Identify Transposon Boundaries
- TSRchitect 1.20.0 - Promoter Identification from large-scale TSS Profiling data
- TSSr - Comprehensive Analyses of Transcription Start Sit (TSS) data
- TTS mapping - Triplex Target DNA Site Mapping
- TURNIP 1.3 - Detection of partial SNPs
- Turtle 0.3.1 - Identifying Frequent k-mers with Cache-efficient Algorithms
- TWAIN - Syntenic Gene Finder
- TweenMotif 1.1 - Visualize Locations of a Specified Target Motif
- Twine 20130802 - Find important Sequences in Cis-regulatory DNA
- Twinscan/N-SCAN 4.1.2 - Gene Structure Prediction
- TwoPaCo v0.9.2 - de Bruijn Graph Construction from complete Genomes
- UCHIME 4.2.40 - Chimeric Sequences Detection
- Ulysses 1.0 - Accurate Detection of Low-frequency Structural Variations in large Insert-size Sequencing libraries
- UMAKE 1.0.1 - SNP Calling Pipeline
- UniDPlot 1.2.2 - Detect Weak Similarities between two DNA sequences
- UniGene DLST 1.0 - UniGene Dynamic Local Storage Tool
- UniMoG - Genome Rearrangement
- UniqTag 1.0.0 - Abbreviate Strings to short unique Identifiers
- UnMeRFi - Under-Methylated Region Finder
- UnoSeq 1.0 - Expression Profiling with Next Generation Sequencing without a Reference Genome
- UNWORDS - Compute Absent Words in Genomic Sequences
- UPIC 1.2 - Perl scripts to determine the number of SSR markers to run
- USEARCH 11.0.667 / UCLUST / UBLAST - Sequence Search & Clustering
- USeq 9.2.3 - Analyze Next Generation Sequencing data from Illumina, SOLiD, and 454 platforms
- UTGB Toolkit 1.5.8 - Personalized Genome Browser
- UVWORD - Comparison of DNA Sequences
- V-Phaser 2.0 / V-Profiler 1.0 - Variant Calling and Visualization tools to Identify Biological Mutations in Diverse populations
- VAAL 46233 - Genome Variant Detection
- VAAST 2.0 - Identify Damaged Genes and Disease-causing Variants in Personal Genome Sequences
- ValFold 1.0.0 - Program for the Aptamer Truncation Process
- VaLiAnT - Variant Library Annotation Tool
- VancouverShortR 4.0.16 - Vancouver Short Read Analysis Package
- Varclus - Detection of Positive Selection in Genes and Genomes through Variation Clusters
- VarGeno v1.0.3 - SNP Genotyping from Whole Genome Sequencing data
- VarGibbs 3.0 - Calculates Nearest-neighbour parameters from Melting Temperatures
- VariantClassifier 20100603 - Hierarchical Variant Classifier for Annotated Genomes
- VariScan 2.0.3 - Analysis of DNA Sequence Polymorphisms at the Whole Genome-scale
- VarPlot 1.2 - Similarity Plotting for Alignment of Sequences
- VarScan 2.4.0 - Variant Caller for Short Sequence Reads
- VarSim 0.8.5 - A Simulation Validation Framework for Secondary Analysis in High-throughput Genome Sequencing
- vcf2diploid 0.2.6a / AlleleSeq 1.2a- Personal Genome Constructor
- vcflib 1.0.2 - C++ Library for Parsing and Manipulating VCF files
- VCMap 3.1 - A tool for Comparative Genomics Research
- VCMM 1.0.2 - Variant Caller with Multinomial probabilistic Model
- VDJtools 1.2.1 - Post-analysis of Immune Repertoire Sequencing data
- Vector NTI Viewer 4.0.1 - Read DNA Sequence Data from GenBank, EMBL or FASTA files
- VectorEditor 1.8.1 - Web based DNA Sequence Editing and Analysis tool
- VGO 3.1 - Viral Genome Browser
- Vidjil 201806 - High-throughput V(D)J Repertoire Analysis
- ViKNGS v1.0.0 - Variant Integration Kit for NGS
- Vindel 20150218 - A Simple Pipeline for Checking Indel Redundancy
- VIP 0.1.0 - Metagenomic Identification of Viral Pathogen
- ViQuaS 1.3 - Viral Quasispecies Spectra generated by Next-generation Sequencing
- ViralFusionSeq 20160817 - Discover Viral Integration Events and Fusion Transcripts
- VirFinder v1.1 - Identifying Viral Sequences from Assembled Metagenomic data
- VIRS - A Visual tool for Identifying Restriction Sites
- VirusFinder 2.0 - Detect Viruses and their Integration Sites in Host Genomes
- VirusHunter 0.7 - Analysis of NGS data for Detection of both Novel and Known Virus Sequences
- VirusScan 1.1 - Detect Virus from Next Generation Sequencing data
- VirusSeeker - Virus Discovery and Virome Composition Analysis
- VirusSeq - Detecting Known Viruses and their integration Sites using Next-generation Sequencing of Human Cancer Tissue
- VirVarSeq - a low frequency Virus Variant detection pipeline for Illumina data
- VisCHAINER - Visualizing Multiple Genome Comparisons
- VISCOE 1.0 - Visual Integration Software for Conditional Omics Experiments
- VISDB - Viral Integration Site DataBase
Plugin by dagondesign.com