Posts
- Category: DNA / Genome Analysis (continued)
- eDMR 0.5.1 - R program for Empirical DMR Analysis
- EDSSI - Engineered DNA Sequence Syntax Inspector
- EFFECT 2013 - Automated Construction and Extraction of Features for Classification of Biological Sequences
- EGassembler - Automatic Generation of Consensus Contigs from a set of ESTs
- EGene 1.0 – Automated Pipeline Generation System for Sequence Analysis
- eggNOG-mapper 2.0.1 - Fast Genome-wide Functional Annotation through Orthology Assignment
- EGPred - Eukaryotic Gene Prediction Server
- Ehapp - Estimate Haplotype Frequency from Pooled Sequencing data
- Element 2.0 - Identify Over-represented Motifs across groups of Promoters
- ElemeNT Ver 2 - Tool for Detection of core Promoter Elements
- ELPH 1.0.1 - Estimated Locations of Pattern Hits
- elPrep 5.0.2 - High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling
- eMATRIX 2.0 - Fast Probabilistic Analysis of Sequence Function using Scoring Matrices
- EMD 1.0 - Ensemble Motif Discovery
- EMIRGE v0.61.1 - Expectation-Maximization Iterative Reconstruction of Genes from the Environment
- EMOTIF 3.6 - Sequence Analysis Using Pareto-optimal Discrete Motifs
- Encore 1.31 - Polymorphism-friendly Error Correction
- ENCprime 20140112 - Calculate Codon Usage Bias summary statistic, Nc'
- ENNB - Feature Selection and Comparison in Functional Analysis of Metagenomes
- enoLOGOS 1.0 - Web tool for Energy Normalized Sequence Logos
- Entropic Profiler - Extract and Study Conserved Motifs in Genomes
- EnzymeX 3.3.3 - Determine Restriction Enzymes
- EP3 1.10 - Promoter Prediction Program
- Epi-Speller - Analyze Multiple Genome-wide Profiling Epigenomic data
- EpiExplorer - Exploration and Analysis of large Epigenomic Datasets
- Epigram 0.004 - Predicting Human Epigenome from DNA Motifs
- EpiGRAPH 1.0 - Statistical Analysis and Prediction of Epigenomic data
- epiPaleomix - Inference of Ancient DNA Methylation and Nucleosomal Positioning
- Episomizer - Constuct Extrachromosomal Circular DNA using Whole Genome Sequencing Data
- ERA v1 - Efficient Serial and Parallel Suffix Tree Construction
- ERANGE 4.0a - Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq
- ERDS 1.1 - Calling CNVs from Whole Genome NGS data
- ESEfinder 3.0 - Exon Splicing Enhancer Finder
- EST-PAC - A simple EST management tool and Annotation Pipeline
- ESTate 0.5 - Expressed Sequence Tag Analysis Tools Etc
- ESTminer 0.3 - Gene and Allele Identification
- ESTminer 1.0 - Mining EST Contig and Cluster databases
- EstMoi 1.03 - Estimating Multiplicity of Infection using Parasite Deep Sequencing data
- ESTScan 3.03 - Detect Coding Regions in DNA/RNA Sequences
- EuGène 4.2b - Gene Finder for Eukaryotic Organisms
- EuGene-PP 1.3 - Next Generation Automated Annotation Pipeline for Prokaryotic Genomes
- EukRep v0.6.6 - Classification of Eukaryotic and Prokaryotic sequences from Metagenomic datasets
- EUPAN - Eukaryote Pan-genome ANalysis Toolkit
- EuroForMix 3.3.3 - Statistical DNA Interpretation
- eval 2.2.8 - Analysis of Genome Annotations
- EVIGAN 1.0 - Eukaryotic Gene Predictor
- Evolver - Whole-genome Sequence Evolution Simulator
- EvoPromoter 0.9 - Finding Promoter Regions in Aligned Nucleotide sequences
- ExactSearch - A Fast Plant Motif Search Tool
- ExaLT - Accurate Genome-Wide Survival Analysis
- ExAlt 1.0 - Alternative Exon Isoform Prediction
- EXCAVATOR 2.2 / EXCAVATOR2 1.1.2 / XCAVATOR - Tool for Detecting CNVs from Whole-exome Sequencing data
- ExomeCNV 1.4 - Exome Sequencing-based Copy-number Variation and Loss of Heterozygosity Detection
- ExomeCopy 1.32.0 - Copy Number Variant Detection from Exome Sequencing Read Depth
- Exomiser 12.1.0 - Annotates Variants from Whole-exome Sequencing Data
- eXpress 1.5.3 - Streaming Quantification for High-throughput Sequencing
- extraBinomial 2.1 - Extra-binomial Approach for Pooled Sequencing data
- EXTREME 2.0 - EM algorithm for Motif Discovery
- ExUTR 2017 - Prediction of 3'-UTR Sequences from NGS data
- ezVIR 2 - Human Virus Screening from high-throughput Sequencing data
- F-Seq 1.84 - Feature Density Estimator for High-Throughput Sequence Tags
- FABIAN - Predicting the impact of DNA variants on transcription factor binding
- FaBox 1.61 - Online FASTA Sequences Toolbox
- FACIL 1.0 - Fast and Accurate Genetic Code Inference and Logo
- FACTERA 1.3 - Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm
- FadE 0.0.2 - DNA Methylation Detection
- FAIR - Find Internal Sequence Repeats
- FamAnn 1.0 - Automated Variant Annotation pipeline to facilitate Target Discovery for Family-based Sequencing Studies
- FamilyRelations II 20070330 - Comparative Sequence Analysis
- FANSe 2 - Fast and Accurate Mapping tool for Nucleotide Sequencing Datasets
- FAST 1.7 - FAST Analysis of Sequences Toolbox
- FASTA Composition 1.0 - Find Overall Composition of Sequence
- FASTA Length 1.0 - Finds the Lengths of Sequences in a FASTA file
- FASTA Match Regular Expression 1.0 - Selects FASTA records whose deflines match a Perl Regular Expression
- FASTA Unique Sequences 1.0 - Uniques the Sequences in a FASTA file
- FASTA Unscramble Record Order 1.0 - Sorts one FASTA file according to the deflines of Another
- FastaGrep 2.0 - Search Oligonucleotide Binding Sites from FastA Genomic Sequences
- FASTAParse 0.0.3 - Parsing Module for handling FASTA formatted sequence
- FASTAptamer 1.0.3 - Bioinformatic Toolkit for Combinatorial Selections
- FastEP - Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes
- FastER 1.0 - Identification of Genes with Fast-evolving Regions in closely related Genomes
- Faster2 0.31 - Extensible Tool for working with FASTA and FASTQ files
- FastMotif - Sequence Motif Discovery
- FASTools 1.0.0 - Manipulate Files containing DNA sequences in FASTA and FASTQ format
- FastQ Screen v0.15.0 - Screening Application for High Througput Sequence data
- Fastq-tools 0.8.3 - Small Utilities for working with Fastq Sequence Files
- FastQC 0.11.9 - Quality Control Tool for High Throughput Sequence Data
- FastQValidator 0.1.1a - Validates the Format of Fastq files.
- FastUniq 1.1 - de novo Duplicates Removal tool for paired short DNA Sequences
- FastViromeExplorer - Virus and Phage Identification and Abundance profiling in Metagenomics data
- FASTX-Toolkit 0.0.14 - Short-Reads FASTA/FASTQ files Preprocessing
- FCMM 2.0.0 - Functional Characterization of Multiple Metagenome samples
- fCNV - Detecting Copy Number Variation in a Fetal Genome
- FCP 1.0.7 - Fragment Classification Package
- fdrMotif - Identify Cis-elements by an EM Algorithm Coupled with False Discovery Rate Control
- FEATnotator 1.1.3 - Annotation of Sequence Features and Variation, Facilitating Interpretation in Genomics Experiments
- FetalQuant - Fractional Fetal DNA Concentration Deduction
- FFN - Finding Features for Nucleosomes
- FFS - Database of Drosophila TF DNA Binding Specificities
- FGB 1.0 - Family Genome Browser
- Figaro 1.05 - Novel Vector Trimming software
- Figmop 1.1 - Finding Genes using Motif Patterns
- FinchTV 1.5 - Trace Viewer
- findIR - Detection of Perfect Overlapping and Nested Inverted Repeats in DNA Sequences
- FindPlasmids 20180522 - Find plasmids in Microbial Genome Assembly Files
- FindTail 1.01 - Accurate Detection of Poly(A)/(T) tails and other Homopolymer in RNA-Seq and ESTs
- FineStr 1.0 - Single-base-resolution Nucleosome Positioning
- FIRE 1.1a - Motif Discovery and Characterization program based on Mutual Information
- FirstEF - Human First Exon Finder
- FISH - Fast Indexing for Spaced-seed Hashing
- fitGCP - Fitting Genome Coverage Distributions with Mixture Models
- FiToM / xFITOM / jFITOM 201605 - Detection of Binding Sites in DNA or RNA Sequences
- Fixseq - Universal Count Correction for high-throughput Sequencing
- FLANK 1.0 - Calculate Statistical Parameters governing Over-extension of biologically related Alignments into surrounding random sequences.
- Flash GViewer 0.5 - Customizable Flash Movie to Display Chromosome in Genome
- Flexbar 3.5 - Flexible Barcode and Adapter Removal for Sequencing Platforms
- Flower 0.7.2 - Extracting Information from SFF files
- FlowgramFixer beta - Model the Ion Torrent Sequencing process
- fLPS 2.0 - rapid Annotation of Compositional Biases in Biological Sequences
- FMAP - Functional Mapping and Analysis Pipeline for Metagenomics and Metatranscriptomics studies
- FMFilter 1.0 - A Fast Model based Variant Filtering tool
- FMM 2 - Learn Motifs from Unaligned Sequences
- FOCK 1.0 - Frequency of Oligos
- FOCUS 1.4 - A model to Identify Organisms present in Metagenomes
- FOOTER 2.0 - Find Ammalian Transcription Factor Binding Sites using Phylogenetic Footprinting
- FootPrinter 2.1 / MicroFootPrinter - Phylogenetic Footprinting
- FourCSeq 1.18.0 - Analysis of 4C Sequencing data
- FPB 1.1 - FingerPrint Background removal
- fqtools 1.1 - FASTQ Files Manipulation
- fqtrim 0.9.7 - Trimming & Filtering of Next-gen Reads
- FragGeneScan 1.31 - Predicting Genes in Short and Error-prone Reads
- FrameD 20070223 - Predict Coding Regions in Prokaryotic and Eukaryotic Sequence
- Freddie v0.3.1 - Long Reads Isoform Discovery Tool
- FreeBayes 1.3.1 - Bayesian Genetic Variant Detector
- freeIbis - An Efficient Basecaller for Illumina Sequencers with Calibrated Quality Scores
- freqAnalysis - Identify Statistically Aberrant k-length Nucleotide Motifs in coding DNA sequences
- FSFinder 2.0 - Predict Frameshifting in Genomic Sequences
- FSH - Fast Spaced Seed Hashing
- FSTVAL - Flanking Sequence Tag Validator
- FTG - Fast Fourier Transform based GENE Prediction Server
- FUNC 0.4.9 - Gene Analyzer Application
- FunctionSIM - A Sequencing Simulator for Functional Metagenomics
- FunFrame 0.9.3 - Functional Gene Ecological Analysis Pipeline
- FunSeq2 2.1.6 - Prioritize Regulatory Mutations from Cancer Genome Sequencing
- FunSiP 0.8.1b - Prediction of Functional Sites in DNA
- FusionHunter 1.4 - Identify Fusion Transcripts from Transcriptional Analysis of Paired-end RNA-seq
- FusionMap 20180108 - Detecting Fusion Genes from Next-generation Sequencing data at Base-pair Resolution
- G-InforBIO 1.90 - E-Workbench for Comparative Genome Analysis
- G-Mo.R-Se 20110111 - Gene MOdeling using RNA-Seq
- G4ALL 1.1 - Graphic Contig Analyzer for All Sequencing Platforms
- G4HMM 1.0.0 - G-quadruplex Motif Search using Hidden Markov Models
- GAAS 0.17 - Calculate Accurate Community Composition and Average Genome Size
- GADEM 1.3.1 - Motif Discovery tool for Large-scale Genomic Sequence data
- GADIST - Determine Best Distance Metric for Genome Analysis
- galculator 1.0 - Nucleotide frequency counter
- Galign 1.0 - SNP and Deletion Search tools
- GAME - Utilize Genetic Algorithm to Find Motifs
- GAMP 0.11 - GLOBAL ANALYSIS OF METHYLATION PROFILES
- GangSTR v2.5 - Profiling long STRs from short reads
- GANN 2.0 - Machine Learning tool for the Detection of Conserved Features in DNA
- ganon 1.0.0 - Read Classification tool based on Interleaved Bloom Filters
- GapAdj - Ancestral Genome Inference program
- GAPWM 1.0 - Genetic Algorithm Method for Optimizing a Position Weight Matrix
- Gargammel - Simulation of ancient DNA sequence data
- GASiC r17 - Genome Abundance Similarity Correction
- GASV / GASVPro 20131001- Geometric Analysis of Structural Variants
- GATB 1.4.2 - Genome Assembly & Analysis Tool Box
- GATE 20130701 - Genomic Annotation using Temporal Epigenomic data
- GATK 4.2.2.0 - Analysis Tools for Next-generation DNA Sequencers
- GAZE 0.1 - Integration of Gene Prediction data
- GBrowse 2.54 - Genome Viewer
- GBStools - Bioinformatics tools for Reduced Representation Sequencing data
- GCE 1.0 - Genomic Character Estimator
- gCUP 1.0 - Rapid GPU-based HIV-1 Coreceptor Usage Prediction for Next-Generation Sequencing
- GEB - Genome Environment Browser
- GECKO - GEnetic Classification using k-mer Optimization
- Gecko 2.0 - Gene Cluster Detection in Prokaryotic Genomes
- GEDpm-cg - Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum
- GeIST 2.1.0 - Genomic Integration Site Tracker
- GEMINI 0.30.2 - Integrative Exploration of Genetic Variation and Genome Annotations
- GEMS - Entropy-scaling Search of massive Biological data
- GenAPI v1.0 - Gene Absence Presence Identification tool
- Gene Construction Kit 4.5 - Plasmid Mapping, DNA Cloning Analysis, Vector Manipulation
- Gene Spaghetti 0.7 - Visualize Nucleotide and Amino Acid usage in a Genome
- GeneCOST - Identifying Disease causing Genes
- GeneDesign 5.54 - Codon Manipulation for ORFs
- geneid 1.4.4 - Predict Genes in Anonymous Genomic Sequences
- GeneMark 2.5 - Gene Prediction Programs
- GenePalette 2.0 - Genome Sequence Visualization and Navigation
- GeneParser 2.03a - Find Genes in a Genome
- Genepi 2.0 - Genome Annotation
- genePI 20080506 - Gene promoter identification system
- GeneProf - Analysis of High-throughput Sequencing Experiments
- Gener 1.2 - Chemical Controllers based on DNA Strand Displacement
- GenescanView 1.2 - Visualize Genescan Files
- GeneScreen 20131121 - Rapid Identification of Mutations in multiple DNA Sequence Traces
- GeneSeqer 20140226 - Gene Identification Tool
- GeneSplicer - Detecting Splice Sites in Eukaryotic Genomic DNA
- GeneSyn 1.1 - Detect Conserved Gene Order across Genomes
- GeneTalk - Analyze Human Sequence Variants
- GeneValidator 2.1.11 - Identify Problems with Predicted Genes
- GeneViTo - Genome Visualization Tool
- GenExp /DASgenexp - Web-based Visualization tool that interactively Explore Genomic Database
- GeneZilla 1.22 - GHMM Eukaryotic Gene Finder
- genipe 1.5.0 - GENome-wide Imputation PipelinE
- GenMap 1.3.0 - Fast and Exact Computation of Genome Mappability
- Geno2pheno 3.4 - Estimating Phenotypic Drug Resistance from HIV-1 Genotypes
- GenoCAD 2.3.1 - Design of Plasmids and Synthetic DNA Sequences
- GenoCanyon 1.0.3 - Predict Functional Non-coding Regions in Human Genome
- Genoman - A Library for Accessing and Manipulating Genome Annotation data
- GENOME 0.2 - Rapid Coalescent-based Whole Genome Simulator
- Genome Classifier - Genomic Signature Classifier
- GENOME EXPLORER 1.0 - Comparative Genome Analysis
- Genome Projector - Zoomable User Interface for Molecular Biology
- Genome Randomizer - Generate Random Sequences from Complete Prokaryotic Genomes
- Genome Search Toolkit 0.2.2
- Genome STRiP 2.00.1529 - Discovering and Genotyping Structural Variations using Sequencing data
- Genome Workbench 3.7.1 - View & Analyze Sequence Data
- Genome3D - Annotating Genomes with Structures
- GenomeBrowse 3.0.0 - Free Genome Browser for Exploring Sequencing Pile-up
- GenomeComp 1.3 - Whole Genome Compare & Visulization Tool
- GenomeD3Plot - SVG based Genome Viewer written in Javascript using D3
- Genomedata 1.3.5 - Storage of Multiple Tracks of Numeric data Anchored to Genome
- GenomeFastScreen 1.13.0 - Compi pipeline for Fast Screening of PSS
- GenomeHistory - tool to fully Sequenced Genomes
- genomeIntervals 1.49.0 - Operations on Genomic Intervals
- GenomeJack 3.1 - Genome Viewer for Next-Generation Sequencing
- GenomePixelizer 2003.10.1 - Genome Visualization Tool
- Genomer 0.1.0 - Genome Scaffolding
- GenomeRunner 4.0 - Annotation and Enrichment of Next-Gen Sequencing Data
- GenomeScan 1.0 - Prediction of Gene Structures in Genomic Sequences
- GenomeSmasher 1.0 - Creating Artificial Genomes for Next-gen Sequencing Simulations
- GenomeStudio 2.0.5 - Visualize and Analyze data generated by all of Illumina's platform
- Genometa 0.51 - Rapid Analysis of Metagenomic Datasets
- Genometer 0.9 - Estimating Genome Size in the Presence of Repeats
- GenomeThreader 1.7.3 - Gene Prediction Software
- GenomeTools 1.6.2 - Genome Analysis Software
- GenomeView N42 - Next-generation Genome Browser and Editor
- GenomeVIP v1.2.1 - Cloud based Genome Variant Investigation Platform
- Genomica 3.040710 - Analysis and Visualization Tool for Genomic data
- Genomon ITDetector - Detecting Internal Tandem Duplication from Genome Sequence data
- Genomorama 1.54 - Genome Visualization and Analysis
- GenOO 1.5.1 - A Modern Perl Framework for High Throughput Sequencing analysis
- Genoogle BETA 0.81 - Fast similar DNA sequence Searching Engine
- genoPlotR 0.8.11 - Plot Gene and Genome Maps
- GenoREAD - Sequence Verification of Synthetic DNA
- GenoSkyline 1.2.1 - Tissue-specific Functional Annotation
- GenoTan 0.1.5 - Genotyping of Microsatellite Loci
- GENOVA 1.00 - Genome Visualization and Analysis software for detailed Comparison of Genome Functions
- GenPlay 1.1.0 - Genome Analyzer and Browser
- Genquire 3.4.1 /WinGenquire 1.1 - Genome Annotation Workstation
- GenRGenS 2.1 - Generation of Random Genomic Sequences and Structures
- GENSCAN 20030218 - Identification of complete Gene Structures in Genomic DNA
- GENSENG 0.4 - Detecting CNVs from NGS data
- GenSkew - Genomic Nucleotide Skew Application
- GenVisR 1.22.1 - Genome Data Visualizations
- Gepard 1.40 - Calculation of Dotplots even for Large Sequences
- GEPIS - Gene Expression Profiling in silico
- Geptop 2.0 - Gene Essentiality Prediction tool for COMPLETE-GENOME based on Orthology and Phylogeny
- GERP++ 20110522 - Analyze Evolutionary Rates and Find Constrained Elements in a Multiple Alignment
- GeSICA 1.0.2 - Genome Segmentation from Intra-Chromosomal Associations
- GeSTer - Dentify Terminators in Bacterial Genome Sequences
- GEvolutionS - Genome Evolution Simulation
- GFF-Ex 2.3 - Genome Feature Extraction package
- GFS - Genome-based Fingerprint Scanning
- GibbsModule - Multispecies de novo Identification of Cis-regulatory Motifs and Modules
- Giggle v0.6.3 - Search Engine for large-scale integrated Genome Analysis
- GimmeMotifs 0.14.2 - Systematic de novo Motif Prediction pipeline
- GiRaF 1.0.2 - Find Reassortments in Collections of Influenza Genome Sequences
- Girafe 1.44.0 - Functional Exploration of Aligned Next-generation Sequencing reads
- gKaKs 1.3.0 - Genome level calculate Ka/Ks
- gkm-DNN - gapped k-mer deep neural network
- gkm-SVM 2.0 - Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
- GLAD 2.50.0 - Gain and Loss Analysis of DNA
- glfMultiples 20100616 - GLF-based Variant Caller for Next-generation Sequencing data
- Glimmer 3.02b / GlimmerM 2.5.1 - Microbial Gene-finding System
- GlimmerHMM 3.0.4 - Eukaryotic Gene Finder based on GHMM
- GLOBAL 1.0 - Statistical Significance of Semi-global Block Alignments
- GMA 0.1.5 - Genome Mappability Analysis
- GMATA v2.3 - Genome-wide Microsatellite Analyzing Toward Application
- GMATo 1.2 - Genome Microsatellite Analyzing Tool
- GMD 0.3.3 - Generalized Minimum Distance of Distributions
- GMV 0.1 - Genome Majority Vote Gene Start Correction Software
- GMV 1.0c-beta - Genome Map Viewer
- GMV 1e-93 - Genome Browser for Murasaki
- GO Term Finder 0.86 - Gene Ontology Term Finder
- Goby 3.3.1 / GobyWeb 2.3.1 - Next-generation Sequencing Data Management
- goldMINER 2.0.27 - Use CDD to Automate Sequence Annotation
- GoRAMPAGE - Workflow for Promoter Detection by 5'-read Mapping
- GOST 0.1 - Detect Orthologous Relationship in Microbial Genomes
- GOtcha 200812 - Prediction of Gene Function by Application of Gene Ontology
- GotohScan 2.0 - Gene finding via Semi-global Alignment
- GPU-BSM 2.7.1 - BS-treated Reads Mapping Tool
- GPUmotif - GPU-accelerated ultra-fast and Energy-efficient Motif analysis
- GQL - Using Genome Query Language to uncover Genetic Variation
- GRAFIMO v1.1.4 - GRAph-based Finding of Individual Motif Occurrences
- GrailEXP 6.2 - Grail Experimental Gene Discovery Suite
- GrammR 1.1.0 - Graphical Representation and Modeling of Metagenomic reads
- GRAMMy - Shotgun Metagenomics Analysis
- GraphDNA - DNA Composition Analyse Graphing
- GRAST 1.0 - Genome Reduction Analysing Software Tool
- GRC 1.0 - Annotation tool for Prokaryotic Genomes
- GREAT 4.0.4 - Genomic Regions Enrichment of Annotations Tool
- GreenGenie 2 - Predicting Genes in Chlamydomonas Reinhardtii
- Gremlin - Genome Rearrangement Explorer with Multi-Scale, Linked Interactions
- Grid Map 3.0a-beta - Displays Genome Mapping Data in a Grid Format
- GRIL 1.0.0 - Genome Inversion and Rearrangement Locator
- GRIMM 2.01 / MGR 2.03 - Multiple Genome Rearrangements / In Man and Mouse
- GRISOTTO - Motif Discovery Tool
- groHMM 1.26.0 - Analysis of GRO-seq data
- growthpred 1.07 - Prediction of Growth-related Traits in Microbes from Genomic and Metagenomic data
- GSA v1.0 - Genomic Scar Analysis
- GSDS 2.0 - Gene Structure Display Server
- gSearch - Search tool for Whole-genome Sequencing
- GT-Scan / GT-Scan2 - Identifying unique Genomic Targets
- GUPPY 0.988 - Visualize Sequence Annotation Data
- GView 1.7 - Display and Navigate Bacterial Genomes
- GWFASTA - FASTA search in Eukaryotic and Microbial Genomes
- GWIPS-viz - Genome Wide Information on Protein Synthesis
- H3M2 20131219 - Detection of ROH from Whole-exome Sequencing data
- h5vc 2.27.1 - Scalable Nucleotide Tallies with HDF5
- HadoopCNV - MapReduce-based Copy Number Variation Caller for Genome Sequencing data
- Hammer 0.2 - Error-correction of High-throughput Sequencing Datasets
- HaMStR 13.2.6 - Hidden Markov Model based Search for Orthologs using Reciprocit
- HapCUT2 v1.3.1 - Haplotype Assembly or Haplotype Phasing using Sequence Reads from a Diploid Genome
- Haplofinder 1.1 - Assigns Alleles from the Heterozygous Sequence
- HaploGrep 2.2.9 - Automatic mtDNA Haplogroup Classification
- hapLOHseq 0.1.2 - Detection of Subtle Allelic Imbalance Events from Next-generation Sequencing data
- HaploSearch - Haplotype-sequence Two-way Transformation
- Haplotter - Explore the Evidence for Recent Positive Selection in the Human Genome
- Harvest 1.1.2 - A Suite of Core-genome Alignment and Visualization tools
- HattCI 200160218 - Identification of attC sites in large DNA data sets
- HECTOR 1.0 - A Parallel Homopolymer Spectrum based 454 Error Corrector
- HEGESMA 2.0 - Genome Search Meta-analysis ang Heterogeneity testing
- HelitronScanner 1.0 - A Generalized tool for Helitron Identification
- HGTector 2.0b2 - Detection of Candidate HGT-derived Genes
- HHMMiR 1.2 - Prediction of microRNAs using Hierarchical Hidden Markov models
- HighSSR 1.1 - Microsatellites Markers de novo design and Prediction
- HIPPIE 0.0.2b - High-Throughput Identification Pipeline for Promoter Interacting Enhancer elements
- hitchhiking 1.0 - Software for Simulating Selective Sweeps
- HiTEC 20110131 - Accurate Error Correction in High-throughput Sequencing data
- HLAminer 1.4 - Derivation of HLA class I Predictions from Shotgun sequence datasets
- HLAreporter 1.03 - HLA Typing from Next Generation Sequencing data
- HMCan 1.39 / HMCan-diff - Detection of (Differential) Chromatin Modifications in ChIP-seq data
- HMDFinder - Methylation Prediction in Human Genome
- HMM-FRAME 20140724 - Protein Domain Classification for Sequencing Reads with Frameshift Errors
- HMMcopy 0.1.1 - HMM for Detecting Somatic Copy Number alterations in tumour-normal paired Whole Genome Sequencing data
- HMMSeg - Scale-specific Segmention of Continuous Genomic data using HMMs
- HMMSplicer 0.9.5 - Discovery of Splice Junctions in RNA-Seq data
- HnaTyping 1.0.1 - HNA Genotyping From WGS
- Hobbes 3.0 - Genome Sequence Mapping
- HoloVir 1.0 - Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
- Homo 2.0 - Surveying and Visualizing Compositional Heterogeneity across Aligned Sequence data
- HomologMiner 1.00 - Find Homologous Genomic Groups in Whole Genomes
- HomSI v2.1 - Homozygous Stretch Identifier from Next-generation Sequencing data
- Hon-yaku - Identifying Translation Start Sites in Prokaryotes
- hot_scan - Detect Genomic Regions unusually rich in Translocation Breakpoints
- HowDe-SBT 2.00.02 - Sequence Bloom Tree, supporting determined/How Split Filters
- HPeak 2.1 - Define Genome-wide ChIP-enriched Peaks in Human Genome
- HPG pore - Framework for Nanopore Sequencing data
- HPG Variant 1.0 - Characterization of Variants found by Next-Generation Sequencing
- HRIBO 1.5.1 - High-throughput Annotation by Ribo-seq
- HTHmotif - HTH Motif Discovery
- HTSeq 0.13.5 - Process and Analyze data from High-throughput Sequencing (HTS) Assays
- Human Genome 1.0.4 - Obtain information about a known Gene
- Hybrid SHREC - Error Correction Algorithm for Correcting Reads
- Hydra 0.5.3 / Hydra-Multi - Structural Variation Discovery with Paired-end-mapping
- hyfi - software suite for Binding Site Search
- i6mA-Pred - Identifying DNA N6-methyladenine Sites in the Rice Genome
- Ibis 1.1.7 - Improved Base Identification system for the Illumina Genome Analyzer
- ICC 2.0.1 - Insertion, Deletion and Carry-forward Error Correction for Next-generation Sequencing
- iCE 3.5 - View Fingerprint Maps & Associated Data
- ICE 5.9.2 - Biological Part Registry Platform and Tools.
- ICORN 0.97 - Iterative Correction of Reference Nucleotide
- IDEAFIX - Refinement of Variants in FFPE DNA Sequencing data
- IDEG 6.2 - Identification of Differentially Expressed Genes in Multiple Tag Sampling Experiments
- Identitag - Tag-to-gene Mapping
- iDHS-EL - Identifying the location of DHS in human Genome
- iDNA-Methyl - Identifying DNA Methylation Sites via Pseudo Trinucleotide Composition
- iDNA4mC - Identifying DNA 4-methylcytosine sites
- iDNA6mA-PseKNC - Identifying DNA N6-methyladenosine sites
- iDNA6mA-Rice - Detecting N6-Methyladenine Sites in Rice
- iEnhancer-2L - Two-layer predictor for Identifying Enhancers
- iEnhancer-EL / iEnhancer-2L - Identifying Enhancers and their Strength
- iEsGene-ZCPseKNC - Identify eseential Genes based on Z curve pseudo k-tuple nucleotide composition
- IGB 9.1.6 - Visualization for Genome-scale Data
- IGD - A high-performance Search Engine for large-scale Genomic Interval Datasets
- IGIPT - Integrated Genomic Island Prediction Tool
- IGV 2.9.4 / for iPad 1.1 - Integrative Genomics Viewer
- Illuminate 0.6.5 - Analytics toolkit in Python for Illumina HiSeq and MiSeq metrics
- Illuminator 20110419 - Mutation Detection using Short-read Clonal Sequencing
- IMA 3.1.2 - High-throughput Analysis of Illumina’s 450K Infinium Methylation data
- iMADS 1.0.3 - integrative Modeling and Analysis of Differential Specificity
- iMEGES - integrated Mental-disorder Genome Score
- IMEter 2.1 - Calculate the enhancing ability of any specified Intron Sequence
- IMEx 2.0 - Imperfect Microsatellite Extractor
- IMgc - Generates Recombination-free Sequences from Recombination-rich Multiple Sequence Alignments
- IMMpractical 1.2 - Markov Chain Models for Analysis of DNA Sequences
- iMotifs 0.2.5 – Sequence Motif Editor for the Mac
- IMSEQ 1.1.0 - IMmunogenetic SEQuence Analysis
- IMSindel - Intermediate-size Indel Detection tool
- INCA 2.1 - INteractive Codon usage Analysis
- IndelCoder 1.0.1.1 - Recodes the Gaps using the simple Indel Coding algorithm
- Indelz 0.1 - Predict the Effects of Indels and non-sense Mutations
- Indexcov - Fast Coverage Quality Control for Whole-genome Sequencing
- InferCars 20060616 - Reconstruct Contiguous Regions of an Ancestral Genome
- InfoTrim - DNA Read Quality Trimmer using Entropy Created with Python
- inGAP 3.1.1 - Integrated Next-gen Genome Analysis Platform
- inGeno 0.6 - Integrated Genome and Ortholog Viewer
- INSECT 2.0 - Genome-wide Cis-regulatory Modules Prediction
- InsertionMapper 1.1 - Targeted Site Identification from Next-generation Sequencing data with 3-D Pooling
- Insignia 1.2 - Find Unique DNA Sequence
- inSite - Interactive Viewer for Comparing Patterns of Binding Sites across multiple Genomics Regions
- INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1 - Gene Fusion Discovery using Whole Genome and Transcriptome data
- integron_gene_fetch 1.0 - Discovery of Chromosomal Integrons from Metagenomic Sequences
- IntSIM - An Integrated Simulator of Next-Generation Sequencing Data
- iNuc-force - Identify Nucleosome Positions in Genome
- iNuc-PhysChem - Identification of Nucleosomes in S.cerevisiae Genome
- iNuc-PseKNC - Predicting Nucleosomes with Pseudo K-tuple Nucleotide Composition
- InVEx - Ascertain Genes with a Somatic Mutation Distribution showing evidence of Positive Selection for non-silent Mutations
- IonGAP - Integrated Genome Analysis Platform for Ion Torrent Sequence data
- iORI-PseKNC 2.0 - Identify ORIs in the Saccharomyces cerevisiae Genome
- iPAGE 1.2a - Functional and Categorical Enrichment program based on Mutual information
- iParameterEstimation 0.3.1 - Maximum Likelihood Parameter Estimation Package
- iPiG r5 - Integrating PSMs into Genome Browser Visualisations
- iPool-Seq v1.0.3 - Analysis Pipeline for Insertion Pool Sequencing data
- iPro54-PseKNC - Predicting Promoters with Pseudo k-tuple Nucleotide Composition
- iProEP - Predictor for Predicting Promoter
- iPromoter-2L 2.0 - Identifying Promoters and their types by multi-window-based PseKNC
- IR 2.8.0 - Calculating the Repetitiveness of DNA Sequences
- iRep v1.10 - Estimating Bacteria Replication Rates based on Population Genome Copy Number Variation
- IRF 3.07 - Inverted Repeats Finder
- iRO-3wPseKNC / iRO-PsekGCC- Identify DNA Replication Origins
- iROS-gPseKNC - Predict the Origin of Replication of the Genome
- iRSpot-EL - Identify Recombination Spots with an ensemble learning approach
- iRSpot-PseDNC - Prediction of Recombination Spots in S.cerevisiae Genome
- iRSpot-TNCPseAAC - Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Scid Components
- Isaac / isaac_aligner 01.15.04.01 / isaac_variant_caller 1.0.7 - Genome Aligner and Variant Caller
- IScan 1.0.0 - Search for Insertion Sequences (ISs), their Inverted Repeats (IRs), and associated Direct Repeats (DRs)
- IsoCon 0.3.2 - Deriving Finished Transcript Sequences from Iso-Seq reads
- Isofinder 20140824 - Isochore Computational Prediction
- isONcorrect - Error Correction of ONT Transcriptomic Reads
- ISSH - Iterative Spaced Seed Hashing
- ITEP 1.1 - Integrated Toolkit for Exploration of Pan-genomes
- iTerm-PseKNC 2.0 - Identifying Terminator
- iTIS-PseTNC - Identifying Translation Initiation Site in Human Genes
- J-Circos - A Java Graphic User Interface for Circos Plot
- JaDis - Compute Distances between Nucleic Acid Sequences
- JAMM 1.0.8 - Peak Finder for NGS Datasets
- JANE - EST Analyzer
- Jannotatix 0.8 - Sequence and Annotation Viewer
- JASPAR 2020 - Transcription Factor Binding Profile Database
- JBrowse2 1.3 - JavaScript Genome Browser
- JDet 1.4.9 - Visualization of Function-related Conservation Patterns in multiple Sequence Alignments
- Jellyfish 2.3.0 - Counting of K-mers in DNA
- JFreq - Frequencies of Short Nucleotide Sequences
- JIGSAW 3.2.10 - Automated Gene Annotation System
- jMOTU 1.0.7 / Taxonerator 0.9 - Analysis of Large DNA Barcode Datasets
- jNMF - Discovery of Combinatorial Patterns
- Jnomics 0.2 - Cloud-Scale Sequence Analysis
- JointSNVMix 0.8.0 - Graphical Model to Analyse Sequence Data from Tumour/normal Pairs
- JoinX 1.12.0 - Tool for Manipulating Genomic Data
- JPOP 0.1 - Prediction of Operon Structures
- JPREdictor 1.23 - Predict Cis-regulatory Elements
- JSpecies 1.2.1 / JSpeciesWS - Measure the Probability if two Genomes belonging to the Same Species
- Jstacs 2.3 - Java Framework for Statistical Analysis and Classification of Biological Sequences
- K-Estimator 6.1v - Calculate the number of Nucleotide Substitutions
- k-mer Tools 20110322 - Variety of Analysis based on Kmers
- KAnalyze 2.0.0 - DNA/RNA Sequence K-mer Toolkit
- KAT 2.4.2 - K-mer Analysis Toolkit
- KCMBT - K-mer Counter based on Multiple Burst Trees
- KCOSS 2021 - A K-mer Frequency Statistics Software
- KEC 20121128 - Error Correction for Pyrosequencing Reads
- keeSeek 0.4.0 - Searching Distant non-existing Words in Genome
- KIRMES 0.8 - Kernel-based Identification of Regulatory Modules in Euchromatic Sequences
- KisSplice 2.4.0-p1 - Local Transcriptome Assembler for SNPs and AS events
- kmacs - the k Mismatch Average Common Substring Approach to Alignment-free Sequence Comparison
- KMC 3.0 - K-mer Counter
- kmerHMM 20120625 - DNA Motif Elucidation
- KNIME 3.1.2 - open-source data Analysis Platform for Next-generation Sequencing data analysis
- Knime4Bio - Custom Nodes for the Interpretation of Next Generation Sequencing data with KNIME
- KnockoffZoom 1.0 / KnockoffGWAS - multi-resolution Localization of causal Variants across the Genome
- Kontaminant - Kmer-based Screening and Filtering tool for Next-gen Sequencing Reads
- kPAL 2.1.1 - K-mer analysis toolkit and Programming Library
- KR 2.0.2 - Efficient Estimation of Mutation Distances from Unaligned Genomes
- Kraken 1.0 - Genomic Coordinate Translator for Comparative Genomics
- Kraken 13-274 - Tools for Quality Control and Analysis of High-throughput Sequence data
- krocus 0.0.15 - Predict MLST directly from uncorrected long reads
- kSNP 3.1.2 - SNP Discovery and SNP Annotation from Whole Genomes
- KvarQ 0.12.2 - Targeted and direct Variant Calling in FastQ reads of Bacterial Genomes
- LANE runner 2.0 - Annotation of de novo Sequenced Transcriptomes
- lapels 1.1.1 - Remapper and Annotator of in silico (pseudo) Genome Alignments
- LargeDEL 0.1 - A large Deletion Finder tool
- LASAGNA-Search 2.0 - Searching for Transcription Factor Binding Sites (TFBSs)
- LASSIE - Linear Allele-Specific Selection InferencE
- LaTcOm - Visualizing Rare Codon Clusters in Coding Sequence
- LayerCake 20171023 - Visual Comparison of Viral Deep Sequencing data
- LedPred 1.7.7 - Learning from DNA to Predict enhancers
- LeeHom 1.2.15 - Bayesian Reconstruction of Ancient DNA Fragments
- LEMMI - Live Evaluation of Computational Methods for Metagenome Investigation
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