Posts
- Category: DNA / Genome Analysis (continued)
- AgileGeneFilter 20120105 - Allows Sequence Variants to be Filtered
- AgileGenotyper 20130204 - SNP Genotyping File data from SAM files containing Exome Sequence data
- AgileKnownSNPFilter 20120105 - Analyses Sequence Variants
- AgileVariantMapper 20160629 - Visualise Sequence Variant data from Whole Exome Data
- AgileVariantViewer 20120105 - Allows Sequence Variants to be interactively Displayed and Filtered
- AgIn 0.9 - Measuring the landscape of CpG methylation of individual Repetitive Elements
- AGMIAL - Annotate Microbial Genomes
- AhoPro - Seach for Overrepresentation of Given motifs in DNA sequences, P-value calculation
- airpg 1.1.4 - Automatically Accessing the inverted Repeats of Archived Plastid Genomes
- AKSmooth 1.0 - Ajusted Local Kernel Smoothing for Bisulfite Sequencing data
- ALEA 1.2.2 - Allele-specific (AS) Epigenomics Analysis
- Alfresco 0.94 - FRont-End for Sequence COmparison
- alfy 1.5 - Alignment-Free local homologY
- Alien_hunter 1.7 - Interpolated Variable Order Motifs for Identification of Horizontally Acquired DNA
- AlienTrimmer 2.1 - Detecting and Removing Contaminant Sequences in both ends of NGSread sequence
- AlignACE 3.0 - Motif Finding
- Allegro 1.0 / Amadeus 1.2 - Motif Discovery Platform
- alpha-CENTAURI 0.2 - Analyze Centromeric Sequences
- ALSE 1.07 - Motif Finding Tool
- Alta-Cyclic 0.2.2 - Base Caller for Illumina/Solexa Genome Analyzer
- AMIGene - Annotation of MIcrobial Genes
- AmpliCoNE - Ampliconic Copy Number Estimator
- AmpUMI - Design of Amplicon Sequencing Experiments utilizing Unique Molecular Identifiers
- ANACONDA 2.0 - Study of Genes’ Primary Structure
- Ancestor v1.1 - Computational Inference of Ancestral Genomes
- AncesTree - Inferring Clonal Evolution of multi-sample Tumor Sequence data.
- AnCorr - Genome Track Analyzer
- ANDES 20120225 - Analysis of Deep Sequencing
- andi 0.13 - Estimating the Evolutionary Distance between closely related Genomes
- ANGLE - Predict Coding Sequences in low quality cDNA
- ANGSD 0.931 - Analysis of Next Generation Sequencing Data
- ANItools 2.0 - Calculating Average Nucleotide Identify (ANI) of pairs of Genomes
- AnnHyb 4.946 / PyAnnHyb 0.021 - Manage Nucleotide Sequences
- AnnoGen 0.0.1 - Annotating Genome-wide Pragmatic features
- annot8r 1.1.1 - BLAST based GO-EC-KEGG Annotation
- ANTHENUC 1.0 - ANalyze THE NUCleic acids
- antiSMASH 6.0.0 - Antibiotics & Secondary Metabolite Analysis SHell
- APEG - Affinity Prediction by Epigenome and Genome
- Apollo 2.6.5 - Genome Annotation Viewer & Editor
- APOLLOH 0.1.1 - HMM for Profiling Loss of Heterozygosity in Whole Cancer Genome Shotgun Sequencing data
- APPLES 20120911 - Analyse Promoter Sequences on a Genome-wide scale
- ARBitrator 1.0 - Retrieval of auto-curated nifH sequences from GenBank
- ArchTEx 1.0.6 - Accurate Extraction and Visualization of Next-Generation Sequence data
- ARDEN 1.0 - Specificity Control for Read Alignments Using an Artificial Reference
- ARGminer - Antibiotic Resistance Gene Miner database
- ArrayMaker 1.1 - Genotyping-by-Sequencing from Aligned Whole Genomes
- ARResT / AssignSubsets 20191110 - Robust Subclassification of Chronic Lymphocytic Leukemia based on B cell Receptor IG stereotypy
- ART 20160605 - Next-generation Sequencing Read Simulator
- Artemis v18.0.3 - Genome Browser and Annotation Tool
- ARTS 0.2 - Accurate Recognition of Transcription Starts in Human
- Asap - Promoter Analysis
- ASAP 1.1.7 - Automated Sequence data Processing on Computer Clusters
- ASAP 1.4.1 - A Systematic Annotation Package for Community Analysis of Genomes
- ASAP 1.4.1 - A Systematic Annotation Package for Community Analysis of Genomes
- ASaturA - Discriminate Amino Acid Substitutions
- ASCAT 2.5.2 – Allele-Specific Copy number Analysis of Tumours
- AscatNGS 4.4.1 - Somatic Copy Number analysis using WGS paired end wholegenome sequencing
- ASCIIGenome v1.16.0 - Text Only Genome Viewer
- ASEQ 1.1.11 - Fast Allele-specific Studies from Next-generation Sequencing data
- ASP 0.3 - Accurate Splice Site Detection
- AssociationViewer 2.0 - Display SNPs in Genetic Context
- ATGme - A Simple DNA Sequence Optimization tool
- ATLAS 2.6a2 - Analyzing your Metagenome data
- Atlas-Link 0.01 - Link Genome Sequence Contigs into Scaffold
- Atlas-SNP 0.9.9.2 - Mapping and SNP Discovery
- Atlas2 1.4.3 / Atlas2Cloud 0.5 - Genome Analysis Suite
- ATRHunter / ATRHunterPlus - Find Approximate Tandem Repeats in a Genomic Sequence
- AUDACITY 0.2 - AUtozygosity iDentification And ClassIfication Tool
- AUGUSTUS 3.4.0 - Gene Prediction for Eukaryotes
- Auto-PSS-Genome v1.5.0 - Automatic Positively Selected Sites Genome
- AutoCSA 1.0 - Automatic Comparative Sequence Analysis
- AutoGRAPH - Web Server for Automating and Visualizing Comparative Genome Maps
- AutoSequin - automatically Annotate Sequences for Bulk Submission to GenBank
- Avalanche Workbench 2.10 - A Visual Bio-pipeline for Biological Data Analysis
- avdist 1.0 - Analyze Haplotype Differences
- AYB 2.11 - Advanced Base Calling for Next Generation Sequencing Machines
- BaalChIP 1.12.0 - Bayesian Analysis of Allele-specific Transcription Factor Binding in Cancer Genomes
- BACH - Gene Composer
- Badger 1.1 - An Accessible Genome Exploration Environment
- BAGEL 0.91 - Bayesian Analysis of Gene EssentiaLity
- Bagheera - Predicting Fungal CUG Codon Translation in Yeast
- BAIT 1.4 - Organizing Genomes and Mapping Rearrangements in Single Cells
- Bakta 1.2.2 - Rapid & Standardized Annotation of Bacterial Genomes & Plasmids
- BALM 1.0.1 - Analyze MBD-seq
- BALSA 2.0 - GPU Accelerated Integrated WGS and WES Secondary Analysis
- BAM_ABS - Bayesian Assignment Method for Ambiguous Bisulfite Short Reads
- bam2mpg 1.0.1 - Bayesian Genotype Caller for NextGen Sequencing Data
- bamchop - Generate Targeted Resequencing Report from BAM File
- BamHash 2.0 - Hash BAM and FASTQ files to verify Data Integrity
- BaMMmotif v2.0 - Bayesian Markov Model motif discovery software
- BamReadCount 0.01 - Calculate Read Count for each region in the input list of Regions
- BAMseek 20110724 - Browse Large BAM and SAM Alignment Files
- bamstats 0.4 - Extract Various Information from BAM Alignmnet files.
- BAMStats 1.25 - Analysis of BAM format Mapping files
- BAMTOOLS 2.5.1 - C++ API and Toolkit for Analyzing and Managing BAM files
- bamUTIL 1.0.14 - Perform Operations on SAM/BAM files
- Bang - Repeat-supressing Search Tool
- BARCE 1.2 - Bayesian Application for Recombination and Gene Conversion Estimation
- BARCODE - A fast Lossless Read Compression tool based on Bloom Filters
- Barcoded Data Preparation Tools - Preparation of Raw Illumina Reads for Further Analysis
- Bareback 1.0 - Barcode Back-Processing for low complexity Illumina libraries
- BarNone - Match barcodes in Sequencing data based on Levenshtein Distance
- BASELINe 1.3 - Bayesian Estimation of Antigen-Driven Selection in Immunoglobulin Sequences
- Basic4Cseq 1.28.0 - an R/Bioconductor package for analyzing 4C-seq data
- BASTA - Bayesian Modeling of DNA copy number amplification data
- BASys 1.0 - Bacterial Genome Annotation
- Batman - Bayesian Tool for Methylation Analysis
- BatMeth 1.04b - Improved Mapper for Bisulfite Sequencing Reads on DNA Methylation
- BATS - A Basic Analysis Toolkit for Biological Sequences
- BayClone / BayClone2 1.1 - A Bayesian Sequence and Copy Number Caller for Subclones Using NGS Data
- BayesCall 0.3 - Basecaller for the Illumina Platform
- BayesMD - Biological Modeling for Motif Discovery
- Bayexer - Demultiplexing Tool for Illumina sequencers
- baySeq 2.26.0 - Identify Differential Expressed Genes
- bbq - Discovering Cis-regulatory Modules
- bbq - Discovering Dis-regulatory modules
- BCALM 2.2.3 - de Bruijn Graph Compacation from Reads
- bcbio 1.2.8 - Best-practice pipelines for fully automated High Throughput Sequencing analysis
- BCM Trace Viewer - Display .scf Traces and Phred Quality values
- BEACON - Automated tool for Bacterial gEnome Annotation ComparisON
- BEAT 1.31.0 - BS-Seq Epimutation Analysis Toolkit
- BEBaC 20130425 - Estimate Bacterial Community Composition from 454 Sequencing data
- BEclear 2.8.0 - Batch Effect Detection and Adjustment in DNA Methylation Data
- Bedshift v1.1.1 - Bedfile Perturbation tool
- BEETL 1.1.0 - Burrows-Wheeler Extended Tool Library
- Bellerophon 1.03 - Detecting Large Scale Genome Rearrangements
- BEST 1.0.1 - Binding-site Estimation Suite of Tools
- BetaScan 2 - Genome-wide Scan for Balancing Selection using Beta Statistic
- BFC - High-performance Error Correction for Illumina Resequencing data
- BFCounter 0.2 - K-mer Counting Software
- bgc 1.03 - Bayesian Estimation of Genomic Clines
- BGF 1.01 - The Beijing Gene Finder
- BiasAway - A tool to Generate Nucleotide Composition-matched DNA sequences
- BIC-seq 2 0.2.4 - Copy Number analysis from Whole-genome Sequencing data
- BIGNASim - Database Structure and Analysis portal for Nucleic Acids Simulation data
- BIGpre 2.0.2 - Quality Assessment software for both Illumina and 454 platforms
- BIGSdb 1.31.5 - Bacterial Isolate Genome Sequence Database
- Bind-n-Seq - Analysis of in vitro Protein–DNA Interactions
- BinDNase - Predicting TF-DNA Interaction Sites using DNase-seq data
- Bio-Tradis 1.4.1 - A set of tools to Analyse the output from TraDIS analyses
- BioBloomTools 2.3.3 - Fast Sequence Categorization tool utilizing Bloom filters
- BioFace 0.02 - Simplified tool for Genetic Analyzes
- biomaRt 2.49.1 - Bridge from R to BioMart databases
- biomc2 1.9 - Detect recombination in DNA Sequence Alignments
- BioParishodhana - integrating BLAST, ClustalW, primer3 and Restriction Digestion tools
- BioScript - Python Library of Bioinformatics Scripts
- BioWord 20120923 - Sequence Manipulation Suite for Microsoft Word
- BiPad - Web Server for Modeling Bipartite Sequence Elements
- BiQ Analyzer 3.0 / BiQAnalyzer HT / BiQ Analyzer HiMod - Tool for DNA Methylation Analysis
- BIRD v1.1.1 - Big data Regression for predicting DNase I hypersensitivity
- BiSA 0.96 - Genomic Regions Binding Sites Analysis
- Biscap and cfdr 0.11 - Scripts for post-alignment Snp-calling and Verification
- BiSeq 1.32.0 - Processing and Analyzing Bisulfite Sequencing data
- Bismark 0.23.1 - Aligner and Methylation Caller for Bisulfite-Seq Applications
- BisPin and BFAST-Gap - Mapping Bisulfite-Treated Reads
- Bisulfighter 20150318 - accurate Detection of Methylated Cytosines and differentially Methylated Regions
- BitSeq 0.7.5 / for R 1.36.0 - Bayesian Inference of Transcripts from Sequencing Data
- Bivartect 1.1.10 - Accurate and Memory-saving Breakpoint detection by Direct Read Comparison
- BLAST2GENE - Gene Analysis in Genomic Regions
- blastGraphic 0.02 - BLAST Graphic Viewer
- BLESS v1p02 - Bloom-filter-based Error Correction Tool for NGS reads
- blockbuster - Detect Blocks of Overlapping Reads
- BLOG 2.0 - Classification of Animal Species with Barcodes
- BLogo 1.0 - Visualization of Bias in Biological Sequences
- bloutminer 0.9.6 – Script for Mining data from BLAST Reports
- BLSSPELLER 1.0 - Exhaustive Comparative Motif Discovery
- Blue 1.1.3 - Short-read Error-correction tool
- BM-BC 1.0 - Bayesian method of Base Calling for Solexa Sequence data
- BM-Map 2.0.1 - Refining Next-Generation Sequencing (NGS) Read Mapping
- Bmap - Efficient and Error-tolerant Sequencing Read Mapping
- BoBro 2.1 - Identifying cis Regulatory Motifs in Prokaryotes
- BOND - Basic OligoNucleotide Design
- BopGenomes - Compares Genomes in terms of the Presence/Absence of short DNA Segment
- BQGB 090528 - Berkeley Quantitative Genome Browser
- BRA - Binary Repeat Align
- BRAT 1.2.4 / BRAT-BW 2.0.1 / BRAT-nova - Bayesian Modeling of Recombination Events
- BRCA Diagnostic - BRCA Gene Testing
- BreakDancer 1.4.5 - Structural Variation Caller for Paired-end Data
- Breakpoint Calculator 0.2.1 - Calculate Breakpoint Counts for each pair and triplet of Genomes
- BreakPoint Surveyor v1.1 - Pipeline for Structural Variant Visualization
- Breakpointer 0.1 - Locate Vreakpoints of SVs from Single-end Reads
- BreakPointer Beta - Pinpoint Rearrangement Breakpoints using Paired end reads
- BreakSeq 1.3 - Structural Variants Annotation and Identification pipeline
- Breakway 0.7.1 - Identify Structural Variations in Genomic Data
- BroadPeak - Broad Peak calling algorithm for Diffuse ChIP-seq Datasets
- BS-SNPer 1.0 - SNP calling in Bisulfite-seq data
- BSeQC 1.4 - Quality Control of Bisulfite Sequencing Experiments
- BSG - Graphical Theoretical Prediction of Transcription Factor Binding Sites
- BSHMM - DNA Methylation Analysis, based on hidden Markov models
- BSMAP 2.90 - Whole Genome Bisulfite Sequence MAPping program
- bsmooth-align 0.8.1 - Analyzing Whole Genome Bisulfite Sequencing (WGBS) data
- BSSM4GSQ 070717 - Generate Training data for Bayesian Splice Site Models
- BStools - Bisulfite Sequencing Tools
- BTP 1.0 - Analyzing Intra-tumor Heterogeneity from High-throughput Sequencing data
- Btrim - Trim Adapters and Low Quality Regions in Reads
- Bubbleparse - Detecting variants directly from Next-generation Reads
- BubbleTree 2.14.0 - CNV Analysis in groups of Tumor Samples
- BW4SA - Burrows-Wheeler Transform for Sequence Analysis
- BWASP - Bisulfite-seq data Workflow Automation Software and Protocols
- CAFE 1.0 - aCcelerated Alignment-FrEe sequence analysis
- CAIcal 1.4 - Assess Codon Usage Adaptation
- Cake 1.0 - Somatic Mutation Discovery
- CAMBer 2 - Comparative Analysis of Multiple Bacterial Strains
- CAMBerVis 1.5 - Visualization of Comparative Analysis of multiple Bacterial Strains
- CandiSSR - Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences
- CANGS 1.1 - Process & Anylyze 454 GS-FLX data in Biodiversity studies
- CANOES 0.1 - Detecting CNVs from Exome Sequencing data
- CapFilter - Analysis tool for Identifying high Confidence Transcription Start Sites
- CARMA 1.0 - Copy Aberration Regional Mapping Analysis
- Casboundary v1.0.1 - Automated Definition of integral CRISPR/Cas Cassettes
- CASPER 0.8.2 - Context-Aware Scheme for Paired-End Read
- CASSIS / SMIPS 201511 - Prediction of Secondary Metabolite Gene Clusters in Eukaryotic Genomes
- Cassis 1.0 - Detect Genomic Rearrangement Breakpoints
- CAT 1.3 - Composition Analysis Toolkit
- cBar 1.2 - Identification of Chromosomal Sequence Fragments from Metagenome data
- cbc 2.0 - Compression of Aligned Reads via Improved Modeling
- CCAT 3.0 - Control based ChIPSeq Analysis Tools
- cdbfasta /cdbyank 20100722 - Fasta file Indexing and Retrival tool
- cdbg - Tools for Computing Compressed deBruijn Graph
- cDNA Analysis Package 0.1.0 - Analysis of Annotated cDNAs
- CEAS 1.0.2 - Cis-regulatory Element Annotation System
- CEGMA 2.5 - Annotate Core Genes in Eukaryotic Genomes
- CENTIPEDE beta - Inference of TF Binding Sites
- cERMIT v1.2 - the Evidence Ranked Motif Identification Tool
- CG-Pipeline 0.5- Computational Genomics Pipeline
- CGARS - Cancer Genome Analysis by Rank Sums
- CGAT - Comparative Genome Analysis Tool
- CGAT Apps 0.4.0 - Scripts for Genomics and Next-generation Sequencing Analysis
- cgatools 1.8.0 - Downstream Analysis of Complete Genomics data
- CGHweb 1.0 - Analyze Array_CGH data with Multiple Algorithms
- CgiHunter 1.0 - Exhaustive CpG Island Annotation
- CGL 0.08 - Library designed to Facilitate the use of Genome Annotation
- CHAP 2 - Cluster History Analysis Package
- CheckFrame 1.1 - Check Sequenced Clones for Correct Translation Frame
- ChemGenome 2.1 - Gene Prediction Software
- ChIA-PET 1.0 - Processing of ChIA-PET sequence data
- ChimeraChecker V1.1 - Chimera Checker for Fungal ITS Region
- ChIP-Seq 1.5.5 - ChIP-Seq Analysis server
- ChIPDiff - Genome-wide Comparison of Histone Modification Sites Identified by ChIP-seq
- ChIPMunk v8 - DNA Motif Digger
- ChIPSeq Peak Finder - Find Peaks from ChIPSeq data
- ChIPseqR 1.46.0 - Identifying Protein Binding Sites in High-Throughput Sequencing Data
- ChiTaH - Chimeric Transcripts from High-throughput sequencing data
- ChopSticks - Tool to Improve Resolution of Homozygous Deletion Calls
- Chromas 2.6.6 / ChromasPro 2.1.8 - Sequence & Chromatogram Editor
- ChromoZoom - web-based Genome Browser
- CHROnicle 201503 - Reconstruction of the complete Evolutionary History of Genomes
- Cinteny - Server for Synteny Identification and Analysis of Genome Rearrangement
- Circleator 1.0.2 - Perl-based Genome-associated data Visualization Tool
- circlize 0.4.13 - Circular visualization in R
- Circoletto 20160709 - Visualize Sequence Similarity with Circos
- Circos 0.69-9 - Visualize Genome Data and Information in Circular Layout
- cis-Browser 1.0 - Genome Browser for Cis-regulatory Information
- cis-X v1.5.0 - Search for Activating Regulatory Variants in the Tumor Genome
- CisGenome 2.0 - ChIP-chip and ChIP-seq Data Analysis
- CisGenome Browser 1.1.3 - A Flexible Tool for Genomic Data Visualization
- CisPlusFinder 1.0 - Predict Cis-regulatory modules
- Cistematic 3.0 - Platform for Cis-regulatory Element Analysis
- Cister - Find Motif Clusters in DNA Sequences
- CLAMMS 1.1 - A CNV-calling algorithm for Exome Sequencing data
- CLaMS / iClaMS - Classifier for Metagenomic Sequences
- CLARE - Cracking the LAnguage of Regulatory Elements
- CLARK 1.2.6.1 - Fast and Accurate Classification of Metagenomic and Genomic Sequences
- CLcommunity 3.30 - Microbial Community Analysis
- CLEVER Toolkit 2.4 - Clique Enumerating Variant Finder
- CLgenomics 1.51 - Whole Genomic Analysis
- ClicO FS v2.0.0 - An interactive Web-based service of Circos
- ClineHelpR v1.1 - Genomic Cline Outlier Detection and Visualization
- ClinSeK 1.2e - Targeted Variant Characterization Framework for Clinical Sequencing
- CLIOR v1 - Higher Recall in Metagenomic Sequence Classification Exploiting Overlapping Reads
- ClipCrop - Detecting Structural Variations using Soft-clipping Information
- Clippers 0.0.9 - Deletion Identification Program using Periodic Spaced Seed
- Cloanalyst 201506 - Analysis of Antibody Somatic Genetics
- CLOBB 2.0 - Cluster Sequences on the Basis of BLAST
- ClonalOrigin 1.0 - Recombination Detection in Bacteria
- CloneStudio - Visualization for Synthetic Biology Quality Control
- CLOSE 20150928 - A Toolkit for CNA/LOH Analysis with Sequencing data
- CloudAligner 1.9 - MapReduce based tool for Sequence Mapping
- CloudBurst 1.1.0 - Highly Sensitive Short Read Mapping with MapReduce
- Clover 20120216 - Find Overrepresented Motifs in DNA Sequences
- Cluster-Buster 20100219 - Find Dense Clusters of Motifs in Nucleotide Sequences
- CMap 1.01 - View Comparisons of Genetic & Physical Maps
- CMC 20100422 - Cross-mapping Correction software
- CMF - Contrast Motif Finder
- cn.MOPS 1.32.0 - Mixture Of PoissonS for Discovering Copy Number variations in Next Generation Sequencing data
- CN3D 4.3.1 - 3D Molecular Structure Viewer
- CNAnorm 1.39.0 - Estimate Copy Number Aberrations (CNA) in Cancer Samples
- CNCI v2 - Distinguish Protein-coding and Non-coding Sequences
- CnD 1.3 - Copy Number Variant Caller for Inbred Strains
- CNEFinder - Finding Conserved Non-Coding Elements in Genomes
- CNEr 1.28.0 - Detection and analysis of Conserved Noncoding Elements
- CNOGpro 1.1 - Copy Numbers of Genes in Prokaryotes
- CNT-ILP - Integer Linear Program for the Copy-Number Tree Problem
- CNT-MD - Coordinate-descent algorithm for the Copy-Number Tree Mixture Deconvolution
- Co-Bind - Identify Target Sites for cooperatively Binding Transcription Factors
- COCOA 2.8.0 - Coordinate Covariation Analysis
- CodA - Codon Analysis
- CodonLogo - Sequence Logo-based Viewer for Codon Patterns
- CodonO - Analysis of Synonymous Codon Usage Bias
- CodonStatistics - Browse Statistical Information on Genomes
- CodonW 1.4.4 - Codon Usage Analysis
- COGs 201204 - Phylogenetic Classification of Proteins encoded in complete Genomes
- COHCAP 1.38.0 - City of Hope CpG Island Analysis Pipeline
- COLOMBO 4.0 / SIGI-HMM - Statistical Analysis of Sequences of a Genome /Prediction of Genomic Islands in Prokaryotic Genomes
- CoLoRMap - Correcting Long noisy Reads by Mapping short reads
- ComB 2.0.4-1 -Downstream Mapping Analysis for Next Generation Sequence Data
- COMET - Cluster Of Motifs E-value Tool
- coMET - Visualisation of EWAS Results in Genomic Region
- CoMet-Universe - Fast Comparative Functional Profiling of Metagenomes
- CoMeta 0.3 - Classification of Metagenomes using k-mers
- coMotif 1.0 - Identify Transcription Co-regulator Binding Sites in ChIP-seq Data
- CompaGB 1.4 - Genome Browsers Comparison
- CompareProspector - Sequence Motif Finding Algorithm
- COMPETE 0.9.0 - Competitive Occupancy: Multi-factor Profile Evaluation of a Thermodynamic Ensemble
- CompleteGenomicsTools 0.1.1 - A small utility toolset for Complete Genomics Data handling
- ComplexTR 1.2.0 - Discovery of Tandem Repeats having Simple and Complex Pattern Structures
- CompMap - Compressive Short Read Mapping
- Compo - Composite Motif Discovery
- ConDeTri 2.2 - Content Dependent Read Trimmer for Illumina data
- ConsensusFixer 0.4 - Consensus Sequence Caller with Ambiguous bases and in-frame Insertions
- CONSERTING - Copy Number Segmentation by Regression Tree in Next Generation Sequencing
- ConSite - Transcription Factor Binding Site Detection using Phylogenetic Footprinting
- Contemplate 0.2 - Predict CRMs from Comparative Sequence data
- ContEst 1.0.24530 – Estimate Contamination Level in Sequencing data
- CONTIGuator 2.7.5 - Bacterial Genomes Finishing tool for Structural Insights on Draft Genomes
- Contra 2.0.8 - Copy Number Analysis for Targeted Resequencing
- CONTRAST 1.0 - Multiple Sequence de novo Gene Predictor
- CoolBox 0.3.8 - Jupyter Notebook based Genomic data Visualization toolkit
- COPLA - Taxonomic Classifier of Plasmids
- copynumber 1.32.0 - Segmentation of Single- and multi-track Copy Number data by penalized least Squares Regression
- CORA 1.1.5b - compressive-acceleration tool for NGS Read Mapping methods
- Coral 1.4.1 - Error Correction Algorithm for Correcting reads from DNA sequencing platforms
- CoreBoost / CoreBoost_HM - Boosting with Stumps for Predicting Transcription Start Sites / using Histone Modification Signal
- CorQ 20130619 - Quality Score based Identification and Correction of Pyrosequencing Errors
- Correcting Illumina Data
- Correlation Finder - Seek Correlations between Nucleotides in Genomic Sequences
- CORREP 1.53.0 - Multivariate Correlation Estimator and Statistical Inference Procedures
- COSEG 0.2.2 - Identifies Repeat Subfamilies
- CotQuest 1.0 - Nonlinear Regression Analysis of DNA Reassociation Kinetics data
- CoTrix 3.0 - Analysis of complex DNA Banding Patterns
- COUGER 1.8.2 - Identifying Co-factors Associated with Uniquely-bound Genomic Regions
- CovEst 0.5.6 - Estimate coverage from NGS data without Assembly
- CPD r136 - Correlated Pattern Discovery program
- CpGAVAS 2016 - Chloroplast Genome Annotation, Visualization, Analysis and GenBank Submission Tool
- CpGcluster 2.0 - CpG-island Detection
- CpGProD - Predict Mammalian Promoters Associated with CpG Islands
- CpGpromoter - Large-scale Human Promoter Mapping using CpG islands
- CpGviewer 20110406 - Interactive Data Analysis in Bisulphite DNA Sequencing
- Cpipe 2.5.1 - Exome Sequencing Pipeline
- CPModule 0.5 - CRM Detection
- CPTRA 20090207 - Cross Platform Transcriptome Analysis
- CRAIG 1.0 - Gene Predictor
- CRAMER - Cranfield Genome Browser
- CREAD2 - Comprehensive Regulatory Element Analysis & Discovery
- CREST 1.0.1 - uses the soft-clipped reads to directly Map the Breakpoints of SVs
- CRISP 0.2 - Detection of SNVs and Short Insertion/deletion variants from Pooled high throughput DNA sequencing data
- CRISPR-DO 0.1 - Genome-wide CRISPR Design and Optimization
- CRISPR-GA - CRISPR Genome Analyzer
- CRISPRdigger 1.007 - Detecting CRISPRs with better direct Repeat Annotations
- CRISPRdirect - Rational Design of CRISPR/Cas Target
- CRISPResso v2.2.6 - Analysis of Genome Editing Outcomes from Deep Sequencing data
- CRISPRloci - Annotation of CRISPR-Cas Systems
- CRITICA 1.05 - Microbial Gene Finder
- CRM 20111028 - Identification of Conserved Motif Modules
- CRML - Locating Muscle-specific Regulatory Modules in C. elegans Sequences
- Crossbow 1.2.1 - Whole Genome Resequencing Analysis
- CSDeconv 1.03 - Determine Locations of Transcription Factor Binding from ChIP-seq data
- CSP 1.0.0 - Detecting Chimeric Fragments in Dilution-based Sequencing
- cswA 0.01 - Conserved Seq Window Annotater
- CT-Finder / CRISPR-DT - A Web Service for CRISPR Optimal Target Prediction and Visualization
- CTF 0.91 - CRF-based Transcription Factor Binding Sites Finding System
- CTRD - Computing Translocation Distance between Genomes
- CUDA-EC 1.02 - Fast Parallel Error Correction tool for Short Reads
- CuReSim 1.3 / CuReSimEval 1.1 - Customized Read Simulator / Evaluate Mapping Quality of CuReSim Simulated Reads
- Curves+ 2.6 - Analyzing the Conformation of Nucleic Acid Structures
- cutadapt v3.4 - Remove Adapter Sequences from DNA Sequencing reads
- D-Tailor 20130924 - Automated Analysis and Design of DNA Sequences
- d2Meta - Comparison of Metagenomic Samples Using Sequence Signatures
- d2SBin v1.0 - Improving the Binning of Metagenomic Contigs on d2S Oligonucleotide Frequency Dissimilarity
- DAGchainer 20080206 - Computing Chains of Syntenic Genes in Complete Genomes
- Dalliance 0.13 - Interactive Genome Viewing on the web
- DAMBE 5.3.48 - Sequence Data Analysis in Molecular Biology and Evolution
- damidseq_pipeline 1.4 - An automated pipeline for processing DamID Sequencing Datasets
- DANPOS 2.2.2 - Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing
- DanQ - A Hybrid Convolutional and Recurrent Neural Network for predicting the function of DNA Sequences
- DAS tool 1.1.3 - Recovery of Genomes from Metagenomes via Dereplication, Aggregation, and Scoring Strategy
- DASH 1.0 - Domain Analysis of Symbionts and Hosts
- dbc454 1.43 - Density-based Hierarchical Clustering of Pyro-sequences
- DBChIP 1.36.0 - Differential Binding of Transcription Factor with ChIP-seq
- DBSI - DNA Binding Site Predictor
- DCJ2HP - Bayesian Sampling of Genomic Rearrangement Scenarios via Double Cut and Join
- dd_detection - Detecting Dispersed Duplications in High-Throughput Sequencing Data
- DecGPU 1.0.7 - Distributed short read Error Correction on GPUs
- DECIPHER 2.20.0 - Decipher & Manage DNA Sequences
- DECOD 1.0.1 - Fast and Accurate Discriminative Motif Finding
- Decombinator 4.0.3 - Tool for Analysing T cell Receptor Sequences
- DeconSeq 0.4.3 - Detect and Remove Contaminations from Metagenomic datasets
- Deep Threshold Tool / Rosetta Tool - Analysis of Ultra-deep Pyrosequencing and Cloning
- Deep4mC - Computational prediction of 4mC sites in the DNA sequences
- DeepARG 1.0.2 - Deep Learning Approach for Predicting Antibiotic Resistance Genes in Metagenomes
- deepEA - Interactive Analysis of Epitranscriptome Sequencing data
- Deeplasmid - Identifying Plasmids in Microbial Isolates and Assembled Metagenomes
- DeepMethyl 20151121 - Predicting DNA Methylation State of CpG Dinucleotide
- DeepMicro - Deep Representation learning for Disease prediction based on Microbiome data
- DeepMod v0.1.3 - Deep-learning tool for DNA Methylation Detection on Nanopore data
- DeepMP - Detect DNA modifications in Nanopore Sequencing data
- DeepNano - Deep Recurrent Neural Networks for Base Calling in MinION Nanopore Reads
- DeepSEA 0.94c -Deep learning-based algorithmic framework for Predicting Chromatin Effects
- DeepVariant 1.2.0 - Highly Accurate Genomes With Deep Neural Networks
- DeeZ 1.9-beta2 - A tool for Compressing SAM/BAM files
- deFUME 1.0 - Dynamic Exploration of Functional Metagenomics Sequencing Data
- deFuse 0.8.2 - Gene Fusion Discovery using RNA-Seq Data
- Degoligo - Determine the Probability of a Degenerate Oligonucleotide Sequence
- DELLY 0.8.7 - integrated Split-read and Paired-end based Structural Variant Discovery in Deep sequencing data
- DEME 1.0 - Motif Discovery using Positive & Negative Examples
- deML v1.1.3 - Maximum Likelihood Demultiplexing for NGS data
- deNOPA - decoding Nucleosome Positions sensitively with Sparse ATAC-seq data
- detectIR 20150213 - Detection of Perfect and Imperfect Inverted Repeats
- DGE-EM 1.00 - Accurate Estimation of Gene Expression Levels from DGE Sequencing Data
- DGRscan - Identification of Diversity-generating Retroelements systems
- DIAL 20110606 - De novo Identification of Alleles
- DiffMut - Differential Mutational Analysis
- DiMmer - Detection of differentially Methylated Regions
- DiMO 1.6 / DAMO- Discriminative Motif Optimizer
- Dimont - de-novo Motif Discovery tool
- DiNAMO 1.0 - Discriminative DNA IUPAC motif discovery tool
- DiProGB 20100209 - The Dinucleotide Properties Genome Browser
- DIPS 1.1 - Find Discriminative PWM Motifs
- DiscoverY - Y-contig Identification from Whole Genome Assemblies
- Discrover 1.6.0 - Discover Discriminative Sequence Motifs
- DISMISS - Detection of Stranded Methylation in MeDIP-Seq Data
- DistAMo 1.0 - Distribution Analysis of DNA Motifs
- DistG - Distribution Graph
- DistMap 1.0 - A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster
- DivE - Lineage-specific Selection Finder
- DIYA 1.0.1 - Microbial Genome Sequences Annotation
- DMAP - Differential Methylation Analysis Package
- DME 1.0.0 - Discover Transcription Factor Binding Site Motifs
- DMEAS 2012 - DNA Methylation Entropy Analysis Software
- DMI - Driver Mutation Identification
- DMINDA 2.0 - DNA Motif Identification and Analyses
- DNA Baser 5.15 - DNA Sequence Assembly & Analysis
- DNA Chromatogram Explorer Lite 3.2 - View, Edit & Convert Chromatogram
- DNA Counter 1.0.2 - Caculate Proportions of A,C G, T ,CG, AT in DNA Sequence
- DNA for Windows 2.51 - DNA Sequence Editing & Analysis Program
- DNA Master 5.22.1 - DNA sequence editor and analysis package
- DNA Melting 20080207 - Computations on DNA melting
- DNA Slider - Tests Heterogeneity in the Polymorphism-to-divergence Ratio among Different Regions of a Gene
- DNAA 0.1.2 - Analysis Package for Short-read Next Generation Sequencing
- DNAApp 1.2.7 - Mobile Application for Sequencing Data Analysis
- DNAatGlance - Detection of Large-scale Genomic Regularities by Visual Inspection
- DNACLUST r3 - Cluster Millions of short DNA sequences
- DNAFSMiner - DNA Functional Site Miner
- DNAmelt r23 - Compute DNA Melting Properties
- DNAmend 1.02a - Create Virtual DNA Constructs
- DNAPlotter 1.11 - Circular & Linear Interactive Genome Visualisation
- DNAscan 0.1 - Personal Computer compatible NGS Analysis, Annotation and Visualisation
- DNAshape / DNAshapeR 1.0 - High-throughput DNA Shape Prediction
- DnaSP 5.10.01 - Analysis of Nucleotide Polymorphism from Aligned DNA Sequence Data
- DNAStrider/LabStrider 1.59.2 - DNA Analyze software
- DNAux 3.0 - Generate Random DNA Sequences & Compute Overlapped Sequence
- DNAzip - DNA Sequence Compression using a Reference Genome
- DNemulator 20 - Simulating DNA Sequencing Errors, Polymorphisms, Cytosine Methylation and Bisulfite Conversion
- DNMFilter 0.1.1 - De Novo Mutation Filter
- DNN-HMM - De novo Identification of Replication-timing Domains in the Human Genome
- DODO - DOmain based Detection of Orthologs
- DOTS-Finder - Driver Oncogenes and Tumor Suppressors Finder
- DRACK 3.1 - Differential Restriction Analysis
- Dragon Desert Masker -Transcription Initiation Desert Identification
- Dragon PolyA Spotter 1.200 - Predictor of poly(A) motifs within Human Genomic DNA sequences
- Dragon TIS Spotter 1.1 - Search for Translation Initiation Sites (TISs) in Arabidopsis Genomic Sequences
- draw+sneakpeek - DNA Resequencing Analysis Workflow
- dREG - Detection of Regulatory DNA Sequences using GRO-seq Data
- dRep 3.2.2 - De-replication of Microbial Genomes
- DRIM - Discover Motifs in a list of ranked DNA sequences
- DRIMM - Duplication and Rearrangement in Multiple Mammals
- DRIMust 1.0 - Discovering Ranked Imbalanced Motifs using suffix trees
- DriverNet 1.0.0 - Predict Functional Important Driver Genes in Cancer Genome
- DSD 20190308 - DNA Strand Displacement Simulator
- DSK 2.3.3 - K-mer Counting software
- DSM 20140113 - Distributed String Mining Framework
- DSS 2.40.0 - Dispersion Shrinakge for Sequencing data
- dSSpred - Eukaryotic Donor Splice Site Prediction
- DUDes v0.08 - Top-down Taxonomic profiler for Metagenomics
- DynaMIT 1.1.5 - Dynamic Motif Integration Toolkit
- E-MEM 1.0.0 - Efficient computation of Maximal Exact Matches for very large Genomes
- E-TALEN 2.5 - Design TALENs for Genome Engineering
- ea-utils 1.1.2-621 - FASTQ processing utilities
- EAGER 1.92.37 - Efficient Ancient Genome Reconstruction
- EASER 1.7.0 - Ensembl Easy Sequence Retriever
- EasyGene 1.2c - Prediction of Genes in Prokaryotes
- eBAS 3.6 - eMOTIF Batch Analysis Suite
- EBCall - Empirical Bayesian framework for Mutation Detection from Cancer Genome Sequencing data
- EBVariant 1.0 - An Empirical Bayes Testing Procedure for Variants Detection in Next Generation Sequencing
- EC - an efficient Error Correction algorithm for Short Reads
- ECHO 1.12 - Reference-free Short-read Error Correction Algorithm
- ECR Browser - Interactive Browser of Genome Conservation and Evolution
- EDGAR 3.0 - software platform for comparative Genomics
- EDGE-pro 1.3.1 - Prokaryotic Transcriptome Analysis system
- EDGI - Discovers Transcriptional Regulatory Regions in Drosophila Genes
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