Posts
- Category: DNA / Genome Analysis (continued)
- LEPSCAN 1.0.6 - Searching Latent Periodicity in DNA sequences
- Lever 2.0 - Maps Metazoan DNA Regulatory Motifs to sets of Genes
- libGenome 1.3.1 - C library for Developing Sequence Analysis
- LIBRA - Detecting Similar Patterns called Motif on DNA Sequences
- libStatGen 1.0.14 - C++ Library for Handling and Analyzing Next Generation Sequencing and Genotyping Data
- Lighter 1.1.2 - Fast and Memory-efficient Sequencing Error Correction without Counting
- LikelyBin 0.1 - Metagenomic Binner
- LinkedSV - SV Detection on linked-read Sequencing data
- LiRA - Linked Read Analysis
- LIS alignment - Parse BLAST output using the LIS (Longest Increasing Subsequence) algorithm
- LmCGST 1.0 - Molecular Characterization with Next-generation Sequence data
- LobSTR 4.0.4 - Profiling STRs in Personal Genomes
- LocalMotif 1.0 - Discover Transcription Factor Binding Motifs
- LocalNgsRelate - Inferring IBD sharing along the Genome between pairs of individuals from low-depth NGS data
- LocaMo Finder - Predicting local Enrichment of Transcription Factor Binding sites
- LOCK 1.2 - Locater of Oligos
- LocRepeat - Finding Regions of Pseudo-periodic Repeats
- LOCUS - Evidence-based Gene Finding algorithm
- LocusZoom 1.3 - Visualization of Genome-wide Association Scan Result
- LongGF v0.1.2 - Detection of Gene Fusion by long-read Transcriptome Sequencing
- LookSeq 2 - Alignment Visualization, Browsing and Analysis of Genome Sequence data
- LoQuM 0.2 - LOgistic Regression tool for Calibrating the QUality of Short Read Mappings
- LoRDEC 0.9 - A Hybrid Error Correction program for long, PacBio Reads
- LRCstats - Evaluating Long Reads Correction tools
- LRMotifs 1.0 - Logistic Regression-Based DNA Motif Discovery
- LRSDAY v1.6.0 - Long-read Sequencing Data Analysis for Yeasts
- LSA - Metagenomic Read Partitioning by Latent Factor analysis
- LSC 2.0 - Long Read Error Correction, Demonstrated for cDNA Analysis
- LSGSP - Large-Scale Genome Sequence Processing
- LTR_Finder 1.0.5 - Find Full-length LTR Retrotranspsons in Genome Sequences
- LTR_STRUC - LTR Retrotransposon Structure program
- LTRsift 1.0.2 - Postprocessing of de novo predicted LTR Retrotransposon Annotations
- LuceGene 1.4 - Search System for Genome & Bioinformatic Databases
- Lumpy 0.3.1 - Structural Variant Discovery
- LW-FQZip - Light-weight reference-based compression of FASTQ data
- lwgv 0.4 - Lightweight Genome Viewer
- LymAnalyzer 1.2.2 - Analysis TCR/IG Repertoire from High-throughput Sequencing reads
- M-GCAT 2.0 beta - Detect Highly Conserved Regions in Multiple Genomes with Rearrangements and Repeats
- M3D 1.16.0 - Identifies Differentially Methylated Regions across Testing Groups
- MaCS 0.5d - Markovian Coalescent Simulator
- MACS 2.2.5 - Analyze Data Generated by Short Read Sequencer
- MADAP 2.0 - Clustering Tool for One-dimensional Genome Annotation Data Mapped onto Genome Sequences
- MAGIC 0.6.0 - Integrative and Accurate Comparative Genome Mapping
- MaGnET 2.0 - Malaria Genome Exploration Tool
- MAIRA 0.1.7 - Real-time Taxonomic and Functional analysis of long Reads on a laptop
- MAK 1.94 - Automated MITE analysis
- makeCGI 1.3.4 - Finding CpG Islands from DNA Sequences
- MAKER v3.01.03 - Genome Annotation pipeline
- MAMOT 1.0 - hidden MArkov MOdelling Tool
- Manatee v3r0b1 - Functional Annotation
- MapDamage 2.2.1 - Identifies and Quantifies DNA Damage Patterns in Ancient DNA
- MAPseeker 2.0 - Analysis and Visualization of Multiplexed Accessibility Probing read out through NGS
- MAQGene 0.9.4 - Pipeline for Mutant Discovery
- Marina 1.03 - Identification of Over/under-represented TFBSs given large sets of Promoter-sequences
- MaryGold 0.2 - Variation Analysis of Metagenomic Samples
- MaSC - Mappability-Sensitive Cross-Correlation
- MASE 4.1 - Multiple Aligned Sequence Editor
- MASiVE 20130721 - Mapping and Analysis of SIreVirus Elements
- Mason 0.1.2 - Read Simulator software for Illumina, 454 and Sanger reads
- MAT build 3 - Model-based Analysis of Tiling-arrays for ChIP-chip
- MATCHCLIPS 2 - Identifying the Breakpoints and CNVs
- MatrixCatch 2.7 - Recognition of Composite Regulatory Elements in Promoters
- MB 6.84 - DNA Analysis Program
- MBBC 1.1 - Metagenomic Binning Based on Composition
- MCdet - Detection of Functional Residues
- MCMC_IBDfinder 1.0 - Detect IBD Regions simultaneously in Multiple Individuals
- MCMCcodonsite - Identify Sites under Positive Selection
- mCUDA-MEME 3.0.16 - Motif Discovery software based on MEME
- MCV - Mutation Calling with VAF for Whole Genome Sequencing
- MED 2.1 - Gene Prediction in Prokaryotic Genomes with Multivariate Entropy Distance method
- MeDiChI 0.4.1 - Model-Based ChIP-chip Deconvolution Algorithm
- MeDuSa 1.6 - Multi-draft based Scaffolder
- Meerkat 0.189 - Identify Structural Variations
- MegaDot 0.9 - Large Scale Dot Plotter
- MEGAN 6.21.14 - Metagenome analysis
- MEME 5.0.5 - Discovering Motifs within the Sequences
- MEME-LaB - Motif analysis in Clusters
- MEMOFinder - Finding Consensus Motifs using multiple methods
- MentaLiST v0.2.5 - A fast MLST caller for large MLST schemes
- Mercator 2013.01.11 - Multiple Whole-Genome Orthology Map Construction
- MERCED 1.1 - Systematic Discovery of Cis-regulatory Elements in C.reinhardtii
- Mercury 3.2.1 - Next Generation Sequence Analysis Pipeline
- MESA - MOSLA Error Simulator
- MetaBAT 2.12.1 - Reconstructing Single Genomes from Complex Microbial Communities
- MetaCarvel v1.1 - A Scaffolder for Metagenomes
- MetaCherchant - Analysing Genomic Environment of a Nucleotide Sequence within a Metagenome
- MetaCluster 5.0.1 / MetaCluster-TA 1.2.1 / MetaAnnotator 1.4.4beta - Binning and Annotation Tool for Metagenomic Sequences
- MetaComp - Metagenomic Comparative Analysis Platform
- MetaCompare - Prioritizing Environmental Resistome Risk
- MetaCSST - Metagemonic Complex Sequence Scanning Tool
- MetaDomain 20140716 - HMM-based Protein Domain Classification tool for Short Sequence
- Metafast v1.0.0 - METAgenome FAST Analysis Toolkit
- METAGENassist v2 - Web-based Analytical pipeline for comparative Metagenomic Studies
- MetaGeneAnnotator - Gene Finding program for Prokaryote and Phage
- metagenomeSeq 1.34.0 - Statistical Analysis of Sparse High-throughput Sequencing data
- MetaGUN 1.0 - Gene Prediction in Metagenomic Fragments based on the SVM Algorithm
- MetAl 1.1 - Calculate Metric Distances between Alternative Alignments of the same Sequences
- MetaMeta 1.2.0 - Integrating Metagenome analysis tools to improve Taxonomic Profiling
- MetaObtainer - Obtaining the Specified Species from NGS short reads
- metaorf 1.0 – a very simple Gene Finder
- MetaPhyler 1.25 - Taxonomic Profiling for Metagenomic Sequences
- Metarep 1.4.0 - High-performance Comparative Metagenomics Tool
- metaSNV v2.0.1 - Metagenomic SNV Calling Pipeline
- MetaStorm - Metegenomics Analysis and Visualization
- MetaSV 0.5.4 - Structural-Variant caller for Next Generation Sequencing
- MetaTISA - Translation Initiation Site Annotation for Metagenomes
- Methclone v2 - Dynamic Evolution of Clonal Epialleles
- MethGo - Analyzing Whole-genome Bisulfite Sequencing data
- MethMarker 1.0.680 - Facilitate Design of DNA Methylation Assays
- Methpat 2.0.0 - A program for Summarising CpG Methylation Patterns
- MethPipe 3.4.3 - DNA Methylation Data Analysis Pipeline
- Methy-pipe 2.02 - Integrated Pipeline for BS-seq data analysis
- MethylAction - Detecting Differentially Methylated Regions (DMRs) that distinguish Biological and Disease subtypes
- MethylAid 1.27.0 - Visual and interactive Quality Control of large Illumina 450k data sets
- Methylation plotter - A Dynamic Web tool for Easy Methylation data Visualization
- MethylCoder - Bisulfite-treated Sequences
- MethylExtract 1.9.1 - Methylation Maps and SNV calling from Whole Genome Bisulfite Sequencing Data
- methylFlow 0.1.0-Pre - Cell-specific Methylation Pattern Reconstruction
- methylKit 0.99.2 - R package for DNA methylation analysis
- MethylMix 2.20.0 - Identifying DNA Methylation Driven Genes
- MethylSig 0.99.4 - Whole Genome DNA Methylation Analysis Pipline
- MethylViewer 20120328 - Interactive data analysis of Bisulphite DNA Sequencing to Map Chromatin Structure using DNA Methyltransferases
- MetWAMer 1.3.3 - Translation Initiation Site (TIS) Identification
- mGene 0.1.0 beta - Accurate Computational Gene Finding
- Mgenome 1.0 - Finding the Optimal Trees for Multiple Genome Rearrangement by Signed Reversals
- MGEScan-LTR / MGEScan-non-LTR v2 - Identification of LTR/ Non-LTR Retroelements
- MGIP - Meningococcus Genome Informatics Platform
- MGRA 1.0 - Multiple Genome Rearrangements and Ancestors
- mhsmm 0.4.16 - Parameter Estimation and Prediction for Hidden Markov and semi-Markov models for data with multiple Observation Sequences
- MIA - Matrix Integrative Analysis
- MICheck - Checking of Syntactic Annotations of Bacterial Genomes
- MicrobeCensus 1.1.1 - Average Genome Size Estimation from Shotgun data
- MicrobeGPS 1.0.0 - The Explorative Taxonomic Profiling Tool for Metagenomic Data
- micropan 2.1 - R-package for Microbial Pan-genomics
- Microtaxi - Microbial Taxonomic Identification and Classification Server
- MICSA - Identification of Transcription Factor binding sites in ChIP-Seq data
- MID 20150504 - Detection of Microinversions
- MILLIPEDE 1.1.0 - Model for Identifying Transcription Factor Binding Sites
- MIM - Motif Independent Metric
- MINTIA v1.0 - Metagenomic INsertT BIoinformatic Annotation
- MIP Scaffolder 0.6 - Scaffold Contigs Produced by Fragment Assemblers
- MIRA - Methylation-based Inference of Regulatory Activity
- Miropeats 2.02 – Display DNA Sequence Similarity Information Graphically
- MISA - MIcroSAtellite Identification Tool
- mit-o-matic - Automated Mitochondrial Variation Analysis Pipeline
- MITE-Hunter 201111 - Discovering miniature inverted-repeat Transposable Elements from Genomic Sequences
- MitoAnnotator - Annotating Fish Mitogenomic Sequence
- MitoBank 2.1 - Automatic Retrieval and Parsing of Mitochondrial Genomes
- MitoBreak - Mitochondrial DNA Breakpoints Database
- MitoCounter 1.0.1 - Counting mitochondrial DNA Reads from Whole Genome Sequence
- MitoScape v1.0 - Machine-learning workflow for Aligning mtDNA from NGS data
- MitoSeek 1.3 - Extract Mitochondrial Genome information from Exome Sequencing data
- MitoTool 1.1.2 / MitoToolPy 1.0 - Analysis of Mitochondrial DNA of eight Domestic Animals
- MITSU 1.0 - Stochastic EM for Transcription Factor Binding Site Motif Discovery
- MiXCR 3.0.13 - Analysis of T- and B- cell Receptor Repertoire Sequencing data
- MixSIH 1.0.0 - Haplotype Assembly with Mixture Model
- MLOGD - Detect Overlapping CDSs from Multiple Alignments
- mlRho 2.9 - Estimate the Population Mutation and Recombination Rates from Shotgun-Sequenced Diploid Genomes
- MOABS v1.3.8.7 - Model based Analysis of Bisulfite Sequencing data
- MoAn - Motif Annealer
- mobility 0.1 - Genomic Fluidity Perl & MATLAB Scripts
- Mobster 0.1.6 - Accurate Detection of Mobile Element Insertions (MEIs)
- MOCAT2 2.0 - Analyzing Metagenomics Datasets
- MOCCS 2.0 - Motif Centrality Analysis of ChIP-Seq
- MochiView 1.46 - Genomic Sequences Browser
- mod_bio - Apache modules for Next Generation Sequencing data
- MODEST 0.1.4-10 - MAGE Oligo Design Tool
- MoDIL 1.1 - Detect INDEL Variation with Clone-end Sequencing
- ModuleDigger - An Itemset Mining framework for the Detection of Cis-regulatory Modules
- ModuleMaster 1.1 - Identify Cis-regulatory Modules using Promoter Analysis and Microarray Expression data Regression
- MONKEY 2.0 - Identify Matches to DNA Motifs in Multiple Alignments
- MonSTR 1.0.0 - Toolkit for Calling and analyzing de novo STR mutations
- MOODS 1.9.4.1 - MOtif Occurrence Detection Suite
- MOPAT - Predict recurrent Cis-regulatory Modules from known Motif
- Morpheus 2.0 - Prediction of Transcription Factors Binding Sites based on Position Weight Matrix
- MosaicForecast - Identification of Somatic Mutation from bulk Whole-genome Sequencing data
- MosaicSolver - Determining Recombinants of Viral Genomes from Pileup data
- Mosdepth v0.2.6 - Fast BAM/CRAM Depth Calculation for WGS, Exome, or Targeted Sequencing
- MoSDi 1.3 - Sequence Analysis Toolkit for Bioinformatics
- MOSGA 2 - Modular Open-Source Genome Annotator
- MosLocator - Identification of Mos1 Insertions in the C.elegans Genome
- MOST+ 1.5 - Motif Finding system combing Genomic Sequence and Heterogenous Genome-wide Signatures
- MoTeX - a Word-based HPC tool for MoTif eXtraction
- Motif Search 0.2
- MotifAdjuster - Computational Reassessment of Transcription Factor Binding Site Annotations
- motifanalysis 0.4.0 - Motif Analysis
- MotifBooster - Transcriptional Regulatory Motif Modeling and Discovery
- MotifClick - Motif Finding program
- MotifCombinator - Search for Combinations of Cis-regulatory Motifs
- MotifCut 0.1 beta - Non-parametric graph-based Motif Finding algorithm
- motifDiverge 0.4.12 — Motif Divergence between Sequence Pairs
- MotifFinder 21 - Methylated Motif Finder
- motifGPU 1.0 - GPU-computing Accelerate Motif Analysis
- MotifIndexer - de novo Promoter Motifs Finding program
- MotifOrganizer 0.1 Beta - Cluster large sets of DNA sequence motifs to identify common patterns
- MotifRaptor v0.3.0 - Explore the effect of Genetic Variants on Transcription Factor Binding Sites
- MotifRegressor - Find DNA Sequence Motifs
- MotifSampler 3.2 - Probablistic Motif Detection Approach based on Gibbs Sampling
- MotifScan 1.3.0 - Scan input Genomic Regions with known DNA motifs
- MotifSearch 200502 - Search for DNA binding sites
- MotifSuite 201401 - Probabilistic Motif Detection
- MPBind 2.1 - Predict SELEX-derived Binding Aptamers
- MPFE 1.28.0 - Estimation of Methylation Pattern Distribution from Deep Sequencing data
- Mpileup-tools 1.0 - Tools for Mpileup generation and parsing
- MPscan - Index free Mapping of multiple short reads on a Genome
- mrCaNaVaR 0.51 - Micro-read Copy Number Variant Regions
- MRD - Finding Mutation Regions
- mreps 2.6 - Detect Tandem Repeats in DNA sequences
- MRmediation 1.0.1 - Causal Mediation Method with Methylated Region (MR) as the Mediator
- mRNA by SNP Browser 1.0.1 - Graphical Overviews of Whole-genome Association Study
- MRSfinder 1.0 - Find MAR Recognition Signature in DNA Sequence
- MS4 0.2 - Multi Scale Selector of Sequence Signatures
- MSA 4.05 - Microsatellite Analyzer
- msatcommander 1.0.8 - Locate Microsatellite Repeats, Design Locus-specific Primers, and Tag 'em
- msCentipede 1.0 - Hierarchical Multiscale model for inferring Transcription Factor Binding from Chromatin Accessibility data
- mseq 1.2 - Modeling non-uniformity in Short-read Rates in RNA-Seq data
- MSIsensor 0.6 - Microsatellite Instability Detection
- MSQT 0.7.3 - Multiple SNP Query Tool
- MSS 1.0 - Finding all Maximal Scoring Subsequences
- mtDIS - Mitochondrial DNA Distance analysis program
- mtDNA-Server v2 - Analysis of human Mitochondrial DNA data
- mtDNAmanager - Management and Quality Analysis of Mitochondrial DNA Control Region Sequences
- mtDNAprofiler - Mitochondrial DNA Sequence Analysis Tool
- MU2A 1.0 – Single Nucleotide Variant Annotation
- MuGeN 20060919 - Exploration of Multiple Annotated Genome Portions
- MuGI 1.0 - Multiple Genome Index
- Multifasta Analysis 0.1 - Get Informations about a set of Contigs
- MultiFinder - Meta-analysis Discovery of Tissue-specific DNA Sequence Motifs
- MULTIPROFILER - Subtle Motif Finder
- MultiScan - Motif Scan in Multiple Alignments with Background built from HtBackground
- MUMMIE 0.1 / microMUMMIE - Sequence Analysis in the Post-genomic era
- MuMRescueLite 20090522 - Use the Tag Sequencies of mapped to Multiple Loci to the Genome
- MUNGO 1.0 - Python Library of Sequence Analysis
- Murasaki 1.68.6 - Find Anchors from Multiple Genomes
- MUSA 0.5.6 - DNA Motif Discovery Tool for Simple and Complex Motifs
- MuSeqBox 20210507 - Multi-query Sequence Blast Output Examination
- MuSi - Analysis of Gene Libraries Generated by Dodon-directed Mutagenesis
- Musket 1.1 - Parallel and Scalable Multistage K-mer Spectrum based Error Corrector for Illumina Sequence data
- Mussa 1.1.1 - Multi-Species Sequence Analysis
- MUST v2 - de novo Miniature Inverted Repeat Transposable Element (MITE) Detection Program
- Mutascope 1.0.2 - Analysis software designed for PCR-amplicon Sequencing data
- mutationSeq 4.3.9 - Detect Somatic Mutation from Tumour/normal DNA Pair
- MutationTaster 2021 - Mutation Prediction for the Deep-sequencing Age
- MuTect Beta – Identify Point Mutations
- MutSig Beta - Detect Significantly Mutated Genes
- MuWU v1.1.1 - Mu-seq Workflow Utility
- MyRAST r45 - Annotate Genome
- N-score - Predict Nucleosome Positions from DNA Sequence information
- NAIBR - Novel Adjacency Identification with Barcoded Reads
- NanoARG - Antimicrobial Resistance analysis for Nanopore reads
- NanoCaller 0.3.3 - Variant Calling tool for long-read Sequencing data
- NanoMethViz 1.2.0 - Visualise Methlation data from Oxford Nanopore Sequencing
- NanoMod 0.2.2 - Detect DNA Modifications using Nanopore long-read Sequencing data
- Narcisse 2.3.2 - Mirror View of Conserved Syntenies
- NASP 1.5 - Nucleic Acid Structures Predictor
- NBC - Naive Bayes Classification tool
- NBC 1.0 - Neighborhood Breakpoint Conservation
- Nesoni 0.134 - Swiss Army Knife for NGS SNP calling / RNA-Seq DGE / Read Cleaning
- NeSSM / NeSSMt - Next-generation Sequencing Simulator for Metagenomics / Metatranscriptomics
- NetDyn 1.0 - Simulate Gene Network Growing
- NetGene 2.42 - Intron Splice Sites in Human, C. Elegans & A. Thaliana DNA
- NetSig - Network-based Discovery from Cancer Genomes
- NetStart 1.0c - Translation Start in Vertebrate & A. Thaliana DNA
- NextClip 1.3.1 - Nextera Long Mate Pair Analysis and Processing tool
- NextGenMap 0.5.5 - Map NGS Reads against a Reference Genome
- NextSV 1.9.0 - Structrual Variation Detection from long-read sequencing
- nFuse 0.2.1 - Discovery of Complex Genomic Rearrangements in Cancer
- NGS QC Toolkit v2.3.3 - Toolkit for the Quality Control (QC) of Next Generation Sequencing (NGS) data.
- ngs_backbone 1.4.0 - NGS Analyses
- ngs-bits 2021_03 - Short-read sequencing tools
- NGS-MC - Markovian Inference for Molecular Sequences Using NGS Data
- NGS-Trex - NGS TRanscriptome profile EXplorer
- NGS++ 1.2.1 - C++ library for Manipulating Next Generation Sequencing data
- NgsAdmix 20130625 / FastNGSadmixPCA - Infer Ancestry Proportions from low depth NGS data
- NGSanalyzer 1.0 - Identifying SNV and Indels from Short Read Sequence data
- NGSANE 0.5.2.0 - Analysis Framework for Biological Data from High Throughput Experiments
- ngSeqUtils 1.2.1 - Utility Scripts in Python for Handling Next Generation Sequencing data
- NGSmethPipe 1.4 - A tool to Generate High-quality Methylation Maps
- NGSoptwin 1.0-2 - Estimating Optimal Window Size for analysis of low-coverage Next-generation Sequence data
- ngsplot 2.63 - Global Visualization tool for Next-generation Sequencing data
- NgsRelate v2.0 - Estimating Pairwise Relatedness from NGS data
- ngsShoRT 2.2 - A Next Generation Sequencing Short Read Trimmer
- NGSTools 2.0.0 – Analysis of Next Generation Sequencing (NGS) data
- NGSUtils 0.5.9 - Tools for Next-generation Sequencing Analysis
- NGSView 0.91 - Editor for Next-generation Sequencing data
- NGV 0.1 - Browser for Efficient Display of Large HTS Data Sets
- NHMMFDR 1.0.6 - non-homogeneous Hidden Markov Model based FDR control
- NHR-scan - Predictor of Nuclear Hormone Receptor Binding Sites
- NJtandem - Neighbor Joining Approach for Reconstructing Tandem Duplication History
- NmerFreq - Compute the Frequency of N-mers of that size in the Genome
- NoDe - Error-correcting Algorithm for 454 Pyrosequencing Reads
- Nonpareil 3.3.4 - Estimate Average Coverage and Generate Nonpareil Curves
- normGAM - Remove Systematic Biases in Genome Architecture Mapping data
- NovelSeq 1.0.2 - Novel Sequence Insertions Detection
- NPACT 2.3.1 - N-Profile Analysis Computational Tool
- NPLB 1.0.0 - Learn de novo Promoter Architectures from Genome-wide TSSs
- NPS 1.3.2 - Nucleosome Positioning from Sequencing
- npSeq 1.1.1 - Significance Analysis of Sequencing data
- NSA 3.3 - Nucleotide Sequence Analyzer
- NSeq - Java software for Nucleosome Positioning
- NSMAP 0.1.0 - Spliced Isoforms Identification and Quantification from RNA-Seq
- ntHash 2.0.0 - Recursive Nucleotide Hashing
- Nucleosee - Visual Genome-wide search of Nucleosome Patterns
- Nucleosomes Positioning 3.0 - Prediction by Genomic Sequence
- nucleR 2.24.0 - Non-parametric Nucleosome Positioning
- NUCwave v1 - Generates Nucleosome Occupation Maps
- nuMap - Accurate Prediction of Nucleosome Positioning
- NUPACK - Analysis and Design of Nucleic Acid Systems
- nuScore - DNA Deformation Energy and Nucleosome-positioning Score Calculator
- NuST - Nucleoid Survey Tool
- nxCode 0.1 - DNA Barcode Designer and Decoder
- OBITools 1.2.13 - Scripts and Library for Sequence Analysis
- OCW - Identify Over-represented and Conserved Words
- ODS - Online Diagnosis System for Sanger Sequencing based Genetic Testing
- Off-Spotter 0.2.2 - very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs
- OligoCounter 0.64 - Count Overrepresented 8-14bp Oligonucleotides in DNA Sequences
- Oligonucleotide Search 20v2 - Evaluating Propensity of primers to Hybridize to Similar Sequences
- OMGS - Optical Map-Based Genome Scaffolding
- OmicBrowse 1.4.4 - Genomic Resource Browser
- Omics Pipe 1.1.3 - A Computational Framework for Reproducible Next Generation Sequencing analysis
- OMIGA 1.0 - Optimized Maker-based Insect Genome Annotation
- OMWSA - Detection of DNA repeats using moving window Spectral Analysis
- ONCOCNV 6.9 - Detection of Copy Number Changes in Deep Sequencing data
- OperonDB 2.1 - Database of Predicted operons in Microbial Genomes
- oPOSSUM 3.0 - Analysis of Regulatory Motif over-representation
- Optimizer - A web server utility that optimize a DNA or Protein sequence
- ORCAtk 1.0.0 - Transcription Factor Binding Site Detection using Phylogenetic Footprinting
- Ori-Finder 2.0 - Identification of Replication Origins in Archaeal Genomes
- Orphelia - Predict Genes in Metagenomic Sequencing Reads
- OrthoCluster - Synteny Block Detection
- OrthoMCL 2.0.9 - Genome-scale Algorithm for Grouping Orthologous Protein Sequences
- OSfinder 1.4 - Orthologous Segment Finder
- OTUbase 1.42.0 - Operational Taxonomic Unit based analysis within R
- Otupipe 1.1.9 - OTU Clustering pipeline for Next-gen reads
- overlap - Compute Overlap between two sets of Genomic Features
- OxyGene 1.1.0 - Investigate Oxidative-response Genes in whole Prokaryotic Genomes
- p53scan 1.05 & p63scan - Search for the p53 or p63 Motif
- PACVr 0.9.4 - Plastome Assembly Coverage Visualization in R
- paircomp 1.0 - Ungapped Comparisons of Two Sequences
- Pairoscope 0.4.2 - Display of Paired End Reads
- PALEOMIX 1.3.2 - Characterization of Ancient and Modern Genomes by SNP Detection and Phylogenomic and Metagenomic analysis
- Palingol 1.3 - Programming Language in the Description of Nucleic Acids Secondary Structures
- Pan-Tetris 0.9 - Interactive Pan-genome Visualization
- Panache v1.0.0 - PANgenome Analyzer with CHromosomal Exploration
- PanFP - Pangenome-based Functional Profiles for Microbial Communities
- PanGEA 1.04 - The Comprehensive Gene Expression Analyser
- PanGP 1.0.1 - Pan-Genome Profile Analyze Tool
- PANOW 1.0 - Search of Rare Words in Biological Sequences
- paper-ng-sam - Pipeline for simulating NG-SAM experiments
- ParaBWT 1.0.8 - Parallel Burrows Wheeler Transform Construction
- Paraclu 9 - Find Clusters in Data attached to Sequences
- Parallel-QC 1.0 - A Parallel Quality Control computational engine for NGS data
- PARalyzer 2.0 - PAR-CLIP Data Analyzer
- Parat 0.9.1 - Estimates Site Specific Substitution Rates from a set of DNA sequences
- ParDRe 2.2.5 - Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies
- ParsEval 0.9.2 - Compare Two Sets of Gene Structure Annotations
- ParTIES - PARamecium Toolbox for Interspersed DNA Elimination Studies
- PartiGene 3.0.6 - Generate Partial Genomes Tool
- PASA v2.4.1 - Gene Structure Annotation & Analysis
- PaSS - A PacBio Sequencing Simulator
- PASsiT 1.0 - Post Alignment SNV Tools
- PASTAA - Detecting Transcriptions Factors Associated with Functional Categories
- Patchwork 2.4 / patchworkCG 2.0 / TAPS 2.0 - Allele-specific Copy Numbers Analysis of (CompleteGenomics) Whole Genome Data / for microarray data
- Pathoscope 2.0.7 / Clinical PathoScope 1.0.4 - Species Identification and Strain Attribution with Unassembled Sequencing data
- PathSeq 2.0 – Detect Pathogenic Sequences
- PatMaN 1.2.2 - DNA Pattern Matcher for Short Sequences
- PATO v1.0.2 - Pangenome Analysis Toolkit
- PATRONUS b101 - PATtern Recognition by Optimized Numerical Universal Scoring
- PatSearch - Detection of Patterns and Structural Motifs in Nucleotide Sequences
- Patser v3e - Find Locations of Patterns in Sequence
- Pattern locator - Finding local Sequence Patterns in Genomic DNA Sequences
- PatternBranching / ProfileBranching - Finding Subtle Motifs by Branching from Sample Strings
- PATTERNCNV 1.0 - Detecting Copy Number changes from Exome Sequencing data
- PCI 1.0 - Calculate Barcode Gap Probability of Correct Identification of Species.
- PClouds 1.0 - Identify Repeat Structure in large Eukaryotic Genomes
- PDA 2.0 - Pooled DNA Analyzer
- PDA 20060711 - Pooled DNA Analyzer
- pDRAW32 1.1.144 - DNA Analysis Software
- PEAKS - Positional Footprinting Web Server
- PEMer - Discover SVs by Paired-end Read Mapping
- PEnG-motif 1.0.1 - Detect Motifs within large sequence sets
- PEPATAC v0.10.3 - Pipeline for ATAC-seq Data Processing
- perEditor 20130614 - Create Personalized Genome Sequences
- PerM 0.4.0 - Read-mapping software based on Periodic Spaced Seeds for both Illumina and SOLiD sequencing data
- PersonalGenBank 200610 - Local Sequence Database
- PET-Tool 3.0 - Processing the Sequences generated from PET technology
- PGAP 1.2.1 / PGAP-X 1.0.4 / PGAweb - Pipeline for Pan-genome Analysis
- PGB 1.1 - Personal Genome Browser
- PgSA 1.2 - Index allowing Queries for a collection of Sequencing Reads
- PGT 0.42 - Projection Genomics Toolkit
- PhageFinder v2.1 - Identify Prophage Regions within Bacterial Genomes
- PHAST 20161213 / PHASTER - Fast Phage Search tool
- Phat 20001215 - Find Genes in Eukaryotic Organisms
- Phigaro v2.3.0 - Predicting Phages and Prophages
- PHIRE 1.00 - Reveal Regulatory Elements in Bacteriophage Genomes
- PhiSpy 3.7.8 - Find Prophages in Microbial Genomes
- PHLAWD v1 - Phylogenetic Dataset Construction
- Phobos 3.3.12 - Tandem Repeat search tool for Complete Genomes
- PhylCRM 1.1 - Cis-regulatory Module (CRM) Prediction
- PhyloCon v3b - Phylogenetic Consensus for Regulatory Motif Identification
- PhyloCSF 20121028 / PhyloCSF++ v1.1.0 - Distinguish Protein-coding and Non-coding Regions
- PhyloGibbs 1.2 - Discover Regulatory Sites in a Collection of DNA sequences
- PhyloGibbs-MP 2.0 - Motif Finder in Cis-regulatory Sequences of DNA
- PhyloNet v2b - Motif Discovery at Whole Genome Level
- PHYLOSHOP 1.01 - Predicts 16S rRNA Gene Fragments in Metagenomes
- PHYLUCE 1.7.1 - Software for UCE (and general) Phylogenomics
- PhyME - Find Motifs in sets of Orthologous Sequences
- pibase 1.4.7 - Validational and Comparative Analysis of BAM files
- PICNIC - Predict Integral Copy Numbers In Cancer
- pid 0.9 - Alignment-Free Diversity Computation
- PileLine 1.2 / PileLineGUI 1.3 - Handle Genome Position information in Next-generation Sequencing Studies
- PILER - Genomic Repeat Analysis Software
- pim 0.3 - Alignment-free Estimation of Genetic Diversity
- Pindel 0.2.5b8 - INDEL (insertions and deletions) Detection
- PIntron 1.4.2 - Gene-structure Prediction based on Spliced Alignments of Transcript Sequences.
- PipeMeta Beta 0.44 - Run a de novo Transcriptome Annotation Pipeline
- PIPS 1.1.2 - Pathogenicity Island Prediction Software
- PISAtoolbox 1.0 - Probabilistic Inference with Suffix Algorithms
- pISTil 1.0.6 - Pipeline for Interaction Sequence Tag Identification and Analysis
- PLACNET 1.04 / PLACNETw - Plasmid Constellation Network project
- PlasmidForm 1.2 - Create Plasmid Forms Fast and Simple
- Platypus Conquistador 0.9.0 - Confirming Specific Taxonomic Groups within your Samples
- PLOTREP - Visual Analysis of Dispersed Genomic Repeats
- Pluribus / PluribusFast - Exploring the Limits of Error Correction Using a Suffix Tree
- PMAG - Ancestral Genome Inferrence
- PMDtools 0.5 - Separating Ancient DNA from Modern Contamination
- PMSearch - Poly Matrix Search
- PoissonSeq 1.1.2 - Significance Analysis of Sequencing data based on a Poisson log linear model
- polyadq - Detection of Human Polyadenylation Signals
- PolyAMotif - Predict Poly(A) Motifs in human DNA sequence
- PolyPhred 6.18 - SNP Detection
- Pooling - Next-Generation Sequencing of Heterogeneous Viral Populations using Combinatorial Pooling
- poRe 0.24 - An R package to enable Visualisation of Nanopore Sequencing data
- Poretools 0.6.0 - A Toolkit for Analyzing Nanopore Sequence data
- Possum - Detect Cis-elements in DNA Sequences
- PPFINDER 1.0 - Find Processed Pseudogenes in Genome Annotations
- PPFS 2 - Add on to kSNP for predicting Phenotypes from SNPs in Microbial Genome
- pppbenchmark 1.3 - Promoter Prediction Programs
- PPR v1 - Predict Tandem Repeat Sequence Length Variations
- PRE Mapper 1.0 - Searching Polycomb Response Elements (PREs) in Drosophila
- Precise - Predict Regulatory Cis-acting Elements
- Predector 1.2.3.0 - Dertermine Regulatory Elements in Bacterial Genomes
- PREGO 1.2 -Paired-End Reconstruction of Genome Organization
- PrEMeR-CG - Probabilistic Extension of Methylated Reads at CpG resolution
- preseq 2.0 - Predicting Library Complexity
- pRESTO 0.5.13 - Processing raw reads from high-throughput Sequencing of Lymphocyte Repertoires
- PRIAM 201303 - Sequence Profiles Generated from the ENZYME database
- Primrose 2.17 - Identify Oligonucleotides
- PRINCE v2.3 - VNTR Copy Number Approximation
- PRINSEQ 0.20.4 - Preprocess and Generate Statistics about Sequence data
- PRIORITY 2.1.0 - de novo Motif Discovery
- PriorsEditor 1.0.11 - Create and use Positional Priors in Motif Discovery
- PRISM 1.1.6 / PRISM_CTX 1.0.1 - Pair Read Informed Split Mapper
- PriVar - Prioritizing SNVs and Indels from Next-generation Sequencing data
- Prodigal 2.6.3 - Protein-coding Gene Prediction for Prokaryotic Genomes
- project - Projects Genomic Features onto their Sequences
- Prokka 1.14.5 - Annotate Bacterial Draft Genome
- PromFD 1.0 - Predict Promoter Regions in DNA Sequences
- PROMO - Detection of Putative Transcription Factor Binding Sites (TFBS) in DNA sequences
- Promoter 2.0 - Transcription Start Sites in Vertebrate DNA
- PromoterExplorer - Promoter Identification method based on the AdaBoost algorithm
- proovread 2.14.1 - Large-scale high accuracy PacBio Correction through iterative Short Read Consensus.
- PROPER 1.1 - Integrated Prokaryotic Alternative Transcript Unit Predictor
- ProSOM 2.5 - Promoter Prediction Program
- ProStar - Structural Parameters for Promoter Prediction
- protea 0.09 - Protein Coding Gene Prediction
- Psafe 20120530 - Pooled Sequencing Allele Frequency Estimation
- Pscan 1.5 - MOtif Discovery in Nucleotide Sequences from Co-regulated Genes
- Pscan-ChIP 1.3 - Finding Over-represented Transcription Factor-binding Site Motifs
- PSE-HMM v1 - Genome-wide CNV detection from Next Generation Sequencing data
- PseKNC - Generating Pseudo K-tuple Nucleotide Composition
- PseKNC-General - Generating various modes of Pseudo Nucleotide Compositions
- PseudoDomain 20130916 - Pseudogene Identification tool
- PSM - Pyrogram SNP Miner
- PSPE - Simulate Evolution of Non-coding DNA Sequences
- PSTk-Classifier - Classify DNA using a Bayesian approach
- pSTR Finder - Discover Polymorphic Short Tandem Repeat Markers from Whole-genome Sequences
- PurBayes 1.3 - Bayesian Estimation of Tumor Purity and Clonality
- pwmatch 0.1 - Recognizing Position Weight Matrix hits in a sequence
- Pydna 3.1.3 - Tool for DNA Assembly Strategies using Python
- pyDNase 0.2.4 - a Library for Analyzing DNase-seq data
- Pyicoteo 2.0.7 - Analysis of High-throughput Sequencing data
- PyLOH 1.4.3 - Discovering Copy Number Variations in Cancer Genomes
- PyroHMMsnp 1.1 - SNP Caller for Ion Torrent and 454 Sequencing data
- PyroMap - Maps Pyrosequencing Reads onto Reference Sequences
- PyroTrimmer 1.1 - Preprocessor of Metagenome Sequences
- Qeseq 0.2.2 - multipurpose ChIP-seq Analysis tool
- QmRLFS-finder - Prediction Tool for R-loop Forming Sequences
- qnr 0.8067 - Discover Fluoroquinolone Antibiotic Resistance (qnr) Genes in Fragmented Nucleotide Sequences
- QPLOT 20130627 - Quality Assessment and Diagnosis tool for Sequencing
- QSVanalyser 20121206 - Quantitative Analysis of Sequence Variants
- QuadGT - Joint Variant Calling with de novo and Somatic Mutations
- QualiMap 2.2.1 - Evaluating Next Generation Sequencing Alignment data
- Quality Assessment 0.5 - Analyse the Quality of the Next-generation Reads
- Quality Filter - Filter Sequences based on Phred Quality
- QualSim 0.4 - Quality Score Simulator for Next-gen Sequencer Output
- QuantumClone 1.0.0.6 - Clustering Mutations using High Throughput Sequencing (HTS) Data
- Quarc 1.0 - Analyse a set of Short Read data
- QuasR 1.32.0 - Quantify and Annotate Short Reads in R
- QuEST 2.4 - Quantitative Enrichment of Sequence Tags
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