Posts
- Category: Alignment / BLAST (continued)
- OXBench 1.3 - Evaluate Accuracy of Protein Multiple Sequence Alignment
- PAcAlCI 1.2 - Prediction of Accuracy in Alignments based on Computational Intelligence
- PAGAN2 20190829 - Sequence Alignment and Alignment Extension
- Pairagon 1.1 - Pair-HMM based cDNA-to-genome Alignment
- PAL2NAL v14 - Conversion of Protein Sequence Alignments into Corresponding Codon Alignments
- PalCheck - Online Multiple Palindrome Pattern Matching
- PALMA 0.3.7 - mRNA to Genome Alignments using Large Margin Algorithms
- PALMapper 0.5 - Spliced Alignments of RNA-Seq Reads
- PALS 1.0 - Pairwise Alignment of Long Sequences
- ParaAT 2.0 - Parallel Alignment & back-Translation
- PARALIGN 5.0 - Rapid and Sensitive Sequence Similarity Searches
- Parallel T-Coffee 1.914 - Parallel Multiple Sequence Aligner based on TCoffee
- Parasight 7.6 - Visualize and Analyze Biological Pairwise Alignments
- ParaTree - Parametric Alignment of Trees
- parSRA 1.0 - Portable Framework for the Parallel Execution of Short Read Aligners
- PASH 3.0.6.2 - Large-scale Sequence Comparison Method
- path 20140624 - Protein Back-translation and Alignment
- PathBLAST - Alignment of Protein Interaction Networks
- PatMatch 1.2 - Find Patterns in Peptide and Nucleotide Sequences
- PAUL 2.0 - Protein Distance Matrix Alignment
- PBSuite 150824 - Software for Long-Read Sequencing Data from PacBio
- PCMA - Profile Consistency Multiple sequence Alignment
- PCPMer 3.5.6 - Determine Conserved Regions in multiple Sequence Alignments
- PCSHMM 1.1 - Structural Alignment of RNAs using Profile-csHMMs
- PEANUT 1.3.7 - The ParallEl AligNment UTility
- PECAN 0.8 - Alignment method practical for Large Genomic Sequences
- PeCoP - PSI-BLAST Sequence to find Persistently Conserved Positions
- PFAAT 2.0 - Multiple Sequence Alignments Analysis
- PHMMTS 20070918 - Aligns Sequence to Sequence of Known Secondary Structure
- Phylo-VISTA 2.2 - Visualization of Multiple DNA Sequence Alignments
- PicXAA 1.03 / PicXAA-R 1.0 - Probabilistic Maximum Accuracy Alignment / for RNA Structural Alignment
- PipMaker/MultiPipMaker 20110812 - Alignments of Similar Regions in Sequences
- PLAN 1.0 RC19 - High-throughput BLAST Searches and Managing and Mining Results
- PLAST v2.3.1 - Parallel Local Alignment Search Tool for Database Comparison
- PMFastR - New Approach to Multiple RNA Structure Alignment
- POMAGO - Multiple Genome-wide Alignment Tool for Bacteria
- POP -Gap penaltty optimization
- POSA - Partial Order Structure Alignment
- PoSeiDon - Positive Selection Detection and Recombination Analysis
- PRANK 20170427 / webPRANK - Phylogeny-aware Progressive Sequence Alignment
- PREFAB 4.0 - Protein Reference Alignment Database
- PrimerMatch - PCR Primer Alignment Tools
- Pro-Coffee - Aligns Homologous Promoter Regions
- ProAlign 0.5a3 - Probabilistic Multiple Alignment program
- probA 0.1.1 - Stochastic Pairwise Sequence Alignments
- Probalign 1.4 - Web Server for / Multiple Sequence Alignment
- PROBCONS 1.12 - Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
- ProbeMatch - Rapid Alignment of Oligonucleotides to Genome
- ProDA 1.0 - Protein Multiple Aligner
- ProGraphMSA 20130709 - Fast and Robust Phylogeny-Aware Multiple Sequence Alignment
- PROMALS3D - Multiple Sequence and Structure Alignment Server
- ProPIP - Progressive Multiple Sequence Alignment with Poisson Indel Process
- PROPOSAL - PROtein Comparison through Probabilistic Optimal Structure local ALignment
- ProSeqViewer 1.0.42 - Visualize Sequence and Multiple Sequence Alignment (MSA)
- ProSplign 20170203 - Alignment of Proteins against Genomic Sequences
- ProtDeform 1.0 - Protein Structural Alignment
- Protein-DNA Interface Alignment - Interface Alignment between any Two Protein-DNA complexes
- PRRN 5.2.0 - Multiple Sequence Alignment by Doubly Nested Randomized Iterative Method
- PSAR / PSAR-Align - Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling
- PSAweb - Analysis of Protein Sequence and Multiple Alignment
- PSCE 1.01 - Pairwise Sequence Comparison / Evaluation
- PseudoLasso v2 - Efficient approach to correct Read Alignment for Pseudogene Abundance Estimates
- PSI-BLAST-ISS 1.04 - The PSI-BLAST Intermediate Sequence Search tool
- PyBamView 1.0.8 - Browser-based application for Visualizing Complex Bam Alignments
- Pybedtools 0.8.0 - Python extension to BEDTools
- PyNAST 1.2.2 - Python Nearest Alignment Space Termination tool
- QOD 1.0.2 - Alternative Approach to Multiple Genome Comparison
- QOMA 2.0 - Multiple Sequence Alignment of Protein Sequences
- QPALMA 0.9.3 - Optimal Spliced Alignments of Short Sequence Reads
- QSCORE - Multiple Alignment Scoring Software
- Quasar 1.2 - Score & Rank Sequence-structure Alignments
- QuickAlign 1.03 - Alignment editor for Macinthosh computers
- QuickProbs 1.02 - Multiple Sequence Alignment designed especially for GPU
- RALEE 0.8 - RNA ALignment Editor in Emacs
- RaligNAtor 1.2 - A kind of RNA-related BLAST
- RAPSearch 2.22 - Fast Protein Similarity Search
- Rascaf v1.0.2 - Scaffolding with RNA-seq Read Alignment
- RAUR - Re-alignment of unmapped Reads with base Quality Score
- rbamtools 2.16.17 - An R package for Reading and Writing BAM (Binary Alignment) files
- Re-searcher 1.4 - System for Recurrent Searches of Homologs in Protein Sequence databases
- Readaligner 201211 - Mapping (short) DNA reads into Reference Sequences
- REAL 0.0.31 - REad ALigner for Next-generation Sequencing Reads
- ReAlignerV 8.1.4 - Genomic Alignment Tool & Implementation
- ReBLOSUM - Rectangular BLOSUM matrices
- REFINER 200911 - Refinement of Multiple Sequence Alignments
- ReviSTER 0.1.7 - Revise Misaligned Reads to simple Tandem Repeats
- RevTrans 2.0 - Multiple Alignment of Coding DNA from Aligned Amino Acid Sequences
- RFA 0.1 - Random Field Aligner
- rHAT 0.1.1 - Fast Alignment of Noisy Long Reads with Regional Hashing
- Ribostral 20070223 - RNA Sequence Alignment Analysis program
- RL-CSA 20101023 - Regular-language Constrained Pairwise Global Sequence Alignment
- RMBlast 2.10.0 - RepeatMasker compatible version of NCBI BLAST suite
- rNA 1.0 / mrNA 1.0 / grNA 0.9 - randomized Numerical Aligner
- rna-star 2.3.0e - Spliced Transcripts Alignment to a Reference
- RNAlign2D - Multiple Sequence Alignment of RNA using MUSCLE and Secondary Structure data
- RNAmountAlign - RNA Sequence/Structure Alignment
- RUM 2.0.5_06 - Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper
- SABIC - Protein Structure Alignment Based on Internal Coordinates
- SALIGN r205 - Multiple Protein Sequence/Structure Alignment Server
- SAMBLASTER 0.1.26 - Duplicate Marking and Structural Variant Read Extraction
- SAMMate 2.7.4 / assemblySAM 1.1 - Processing Short Read Alignments in SAM/BAM format / RNA-Seq Assembly and Analysis
- Samo 0.4.1 - Protein Structure Alignment tool based on Multiple Objective Optimization
- SAMSVM 1.01 - A tool for Misalignment Filtration on SAM-format Sequences with SVM
- SAMtools 1.12 - Utilities for Manipulating Alignments in the SAM format
- SANA - Protein Structure Alignment by Neighborhood Alignment
- SAP 1.1.3 - Pairwise Protein Structure Alignment via double Dynamic Programming
- SAPS/SSPA 20110801 - Statistical Analysis of Protein Sequences & Significant Segment Pair Alignment
- SARA-Coffee 1.0.7 - Accurate Multiple RNA Structural Alignment
- SAS-Pro - Sequential and Non-sequential Structure Alignment of Proteins
- Satsuma2 - Whole-genome Synteny Aligner
- SBAL 1.8 - Structure-based Amino Acid Sequence Alignments
- SBG - Sorted Blast Graph
- sBWT 1.0b1 - Burrows–Wheeler transform (BWT) based Fast Indexer/Aligner
- ScalaBLAST 2.4.53 - Multiprocessor Implementation of the NCBI BLAST library
- SCALI - Non-sequential Structure-based Alignment
- SCISSORS - Split-read Aligner
- Se-Al 2.0a11 - Manual Sequence Alignment Editor
- Seal - SEquence ALignment Evaluation Suite
- SEAL 0.4.0rc2 - Read Mapper and Duplicate Remover
- SeaView 5.0.5 - Sequence Alignment and Phylogenetic Tree Building
- SECISaln 1.0 - Create Structure-based Alignments of an extensive dataset of Eukaryotic SECIS Sequences
- secureBlast 1.03 - Controlled access to wwwBLAST
- seg-suite - Manipulate Segments and Alignments
- SeqAlto 0.5-r123 - Fast and Accurate Read Alignment for Resequencing
- Seqotron v1.0.1 - Alignment Editor for Mac OS X
- SeqTools 4.44.1 - A Suite of Tools for Visualising Sequence Alignments
- SequenceServer 2.0.0.rc8 - Set up a Local BLAST Web Server to Search & Share Sequence data
- Sequlator 2013 - Free Multiple Sequence Alignment Editor
- Sequoia 1.0.1 - Align Hpmologous Protein Sequences and Structures
- SeqVis 1.5 - Visualization of Compositional Heterogeneity in Large Alignments of Nucleotides
- SFESA - Shift to Fix secondary structure ElementS in Alignments
- SHE-RA - SHortread Error-Reducing Aligner
- SHiAT 1.1 - Generates Plots of Variation along Sequence Alignment
- SHRiMP 2.2.3 - Align Genomic Reads against Target genome
- SIB-BLAST - Algorithm to Improve Accuracy in PSI-BLAST Searches
- SibeliaZ 1.2.0 - Multiple Whole-genome Alignment based on de Bruijn graphs
- SIBsim4 0.20 - Align an Expressed DNA Sequence with a Genomic Sequence based Sim4
- Sigma 2.0 BETA - Non-coding DNA Sequence Alignment
- Sim4 20121010 - Align an Expressed DNA Sequence with a Genomic Sequence
- sim4cc 20101122 - Cross-Species Spliced Alignment
- SINA v1.2.11 - High-throughput Multiple Sequence Alignment of ribosomal RNA genes
- SlideSort v2 - All Pairs Similarity Search for Short Reads
- SlideSort-BPR 1.0.0 - Finding Differences between Multiple Short-read datasets without Reference Genome
- SMAL - Scaffold-Based Multiple Network Aligner
- SMALT 0.7.6 - Align DNA Sequencing Reads with Genomic Reference Sequences
- SNAP 1.0.4 - Scalable Nucleotide Alignment Program
- SNP-sites 2.5.1 - Finds SNP sites from a multi-FASTA Alignment file
- SNPsplit 0.5.0 - Allele-specific Alignment Sorting
- SnS-Align - Alignment of Distantly related Proteins
- SOCS 2.2 - SOLiD Read Mapper with Bisulfite Sequencing Support
- SPalign / SPalign-NS - Protein Structure Alignment
- SPALN 2.3.3f - Mapping and Alignment of a set of cDNA Sequences onto a Genomic Sequence
- SpEED - Fast Computation of Sensitive Spaced Seeds
- Splign 20150223 - Compute cDNA-to-Genomic / Spliced Sequence Alignment
- SQUARE - Server for Quick Alignment Reliability Evaluation
- Squint 1.02 - Multiple Sequence Alignment Editor
- SRMA 0.1.15 - Sequence Re-alignment for Next Generation Sequencing
- SRmapper 0.1.5 - Genome-hashing Alignment tool
- SSAHA 2.5.5 - Sequence Search & Alignment by Hashing Algorithm
- ssahaEST 1.0.1 - Sequence Search and Alignment by Hashing Algorithm
- SSAHAsnp 1.01 - Sequence Search and Alignment by Hashing Algorithm
- sStu 1.1 - Multiple kinds of Sequence Alignments
- SSU-ALIGN 0.1.1 - Structural Alignment of SSU rRNA Sequences
- SSW - SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications
- STAMP 4.4.2 - Structural Alignment of Multiple Proteins
- Stampy 1.0.23 - Read Aligner capable of Gapped Alignment for Illumina Short Reads
- STAR3D 1.2 / WebSTAR3D / LocalSTAR3D v1 - Alignment of RNA 3D Structures
- StatAlign 3.4 - Bayesian Analysis of Protein, DNA and RNA Sequences
- StatSigMA beta / StatSigMA-w v2 - Computes P-value of (Whole-Genome) Multiple Alignment
- Stellar 1.4.11 - Local Pairwise Aligner
- StrAl 0.54 - Multiple alignments of non-coding RNAs
- Stralign 0.1 - Protein Structure Alignment Tool
- STRAP 20200621 - STRucture-based Sequence Alignment Program
- STRIKE 1.2 - Sequence Alignment Scoring Tool
- SUBOPT - Aligns Two Protein Sequences
- SuiteMSA 1.3.22B - Visual tools for the comparison and analysis of Multiple Sequence Alignments
- Supersplat 1.0 - Spliced RNA-seq Alignment
- Swalign 0.1 - Smith-Waterman Alignment Implementation in C
- SWAPHI 1.0.5 - Smith-Waterman on Intel Xeon Phi
- Swat - Aligning DNA/RNA sequences and Protein sequences
- SWCuda 1.92 - CUDA compatible for Smith-Waterman Sequence Alignment
- SWeBLAST - Look for Recombinations in non-aligned Sequences using BLAST
- SWIFT 1.0.1 / BALSAM 1.3 - Fast Local Alignment Searching
- T-Coffee 13.39.0 - Multiple Sequence Alignment Tools
- T-RMSD - Allows fine-grained Structural Clustering of a given group of related Protein Domains
- tantan 22 - Find Cryptic Repeats in DNA, RNA, and Protein Sequences.
- TAPyR 1.3 beta4 - Tool for Alignment of Pyrosequencing Reads
- TCS - Evaluation and Filtering of multiple Sequence Alignments
- ThermonucleotideBLAST 2.04 - Searching Nucleic Acid-based Assays against Sequence Databases
- ThreadPair 1.1 - Align Membrane Protein Sequences
- TM-align 20150914 - Quick & Accurate Structural Alignment
- Tmod 1.1.1 - Toolbox of Motif Discovery
- Topali 2.5 r3 - Statistical & Evolutionary Analysis of Multiple Sequence Alignments
- TopMatch - Protein Structure Alignment
- TransposonPSI 20100822 - PSI-Blast to Mine (Retro-)Transposon ORF Homologies
- TreeRefiner 1.1 - Refining Multiple Sequence Alignments
- TREMOLO-HCA - Analysis of Distant Relationships between Protein Sequences
- TRIC - Alignment Tool for Targeted Proteomics
- trimAl 1.4 - Tool for Automated Alignment Trimming
- TwinCons - Alignment Score for detection of Ancient Homologies
- Two Sample Logo 1.21 - Calculate Differences between two sets of Aligned Amino Acids or Nucleotides
- Typhon Beta - A Multiple Alignment Indexing Tool
- UnderII - Regulatory Sequences Comparison
- UniAlign - Protein Pairwise Structure Alignment with Evolution and Sequence Information
- UPP - Ultra-large alignments using Phylogeny-aware Profiles
- Vim Alignment highlighting - Vim highlighting files for DNA sequence alignments
- ViroBLAST - BLAST web interface
- VISTA Browser 2.2.47 - Visualize Alignments
- VISTAL - Two-dimensional Visualization tool for Structural Alignments
- ViTO 20031125 - Protein Sequence Structure Alignments
- W-curve - Visualization and Analysis of long Genomic Strings
- Wasabi 20200205 - Powerful Multiple Sequence Alignment Browser
- WeaveAlign v1.2.1 - Multiple Sequence analysis in the presence Alignment uncertainty, using directed Acyclic Graphs
- WHAM 0.1.5 - High-throughput Sequence Alignment
- WinBioinfTools 1.0 - Bioinformatics Tools for Windows High Performance Computing Server
- WOOF - Word-oriented Objective Function for Validation of Sequence Alignments
- xalign 6.1 - Multiple Sequence Alignment
- XMatchView 1.2.5 - Visualize DNA Sequence Alignments.
- XPARAL 2.0a - Parameterized Alignment of Two Sequences
- YAHA 0.1.83 - Long-read Alignment with Optimal Breakpoint Detection
- YAP - Pairwise Sequence Alignment Using Secondary Structures
- YASS 1.15 - Genomic Similarity Search Tool
- zipHMM 1.0.1 - Library for very fast Likelihood Computations for Hidden Markov Models
- ZORRO - Probabilistic Alignment Masking program
- zPicture / multi-zPicture - Dynamic Alignment & Visualization Tool
- Category: Assembly Tools
- A5-miseq 20160825 - de novo Assembly & Analysis of Illumina Sequence data
- ABACAS 1.3.1 - Algorithm Based Automatic Contiguation of Assembled Sequences
- ABySS 2.3.2 - de novo, parallel, paired-end Sequence Assembler
- ABySS-Explorer 1.3.4 - Sequence Assembly Visualization Tool
- ALE 20180904 - Assembly Likelihood Estimator
- AlignGraph - Secondary de novo Genome Assembly guided by closely related References
- ALLPATHS-LG 51750 - Whole Genome Shotgun Assembler
- AMOS 3.1.0 - Whole Genome Shotgun Assembler
- Ananas - A de novo Assembler of RNA-Sequence data
- Anchor 0.3.1 - Post-processing Tools for de novo Assemblies
- Arachne 4.6233 - Whole-genome Shotgun Assembler
- ARBitR - Assembly Refinement with Barcode-identity-tagged Reads
- ARC 1.1.4-beta - Assembly by Reduced Complexity
- ARCS / ARKS v1.2.2 - Genome Assembly Scaffolder with linked and Long Reads
- ARIBA 2.14.4 - Antimicrobial Resistance Identification By Assembly
- ASA3P v1.3.0 - Automatic Bacterial Isolate Assembly, Annotation and Analyses Pipeline
- ASAP - Assemble Species by Automatic Partitioning
- Assemblet 0.1 - Antigenic Variation Assembler
- AssemblX - Toolkit for Rapid and Reliable Multi-Gene Assemblies
- Atlas 2005 - Whole Genome Assembly Suite
- ATLAS GapFill 2.2 - Deals with the Repetitive Gap Assembly problem
- aTRAM 2.4.3 - automated Target Restricted Assembly Method
- AutoAssemblyD 0.1 - Graphical User Interface system for several Genome Assembler
- AutoEditor 1.20 - Automated Correction of Genome Sequence Errors
- AV454 1.0 - de novo Consensus Assembler designed for reads derived from diverse Viral Populations
- Baa.pl 0.20 - use BLAT to ASSESS an ASSEMBLY
- Bandage v0.8.1 - Navigating De novo Assembly Graphs Easily
- bcm-ace-plots - Reads in an Ace format Assembly File produced by the Phrap
- BEAP 0.6 beta - Blast Extension and Assembly Program
- Binnacle - Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins
- BinPacker 1.1 - Packing-Based De Novo Transcriptome Assembly from RNA-seq Data
- BioLign 4.0.6 - Assembly Editor
- BioSequenceAssembler 2.0 - Microsoft Research Sequence Assembler
- BRANCH 1.8.1 - boosting RNA-Seq Assemblies with Partial or related Genomic Sequences
- Bridger 20141201 - RNA-Seq Assembly
- BugBuilder - Microbial Genome Assembly
- BUSCO v5.2.2 - Assessing Genome Assembly and Annotation Completeness with Single-copy Orthologs
- CAFTOOLS 2.0.2 - Tools for the Common Assembly Format (CAF)
- CAP3 / PCAP - Sequence and Genome Assembly Programs
- CAR - Contig Assembly of Prokaryotic Draft Genomes Using Rearrangements
- Celera Assembler 8.3 / Canu v2.2 - Whole Genome Shotgun Assembler
- CEM 0.9.1 - Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads
- Cerulean 0.1.1 - Hybrid Genome Assembler
- CGAL 0.9.6b - Computing Genome Assembly Likelihoods
- Chromonomer 1.13 - Genome Assembly with Genetic Map
- Circlator 1.5.6 - A tool to Circularize Genome Assemblies
- CLC Genomics Workbench 12.0.3 - Assembly & Analysis of Sequencing Data
- clview - Assembly File Viewer
- COCACOLA - Binning Metagenomic Contigs using Sequence COmposition, Read CoverAge, CO-alignment, and Paired-end Read LinkAge
- CodonCode Aligner 9.0.2 - DNA Sequence Assembly & Alignment
- Compartmentalized Assembler - Assembly of Physical Maps
- ConPADE 1.00 - Contig Ploidy and Allele Dosage Estimation
- Contiguity 1.0.4 - Contig Adjacency Graph Construction and Visualisation
- Contrail 0.8.2 - Assembly of Large Genomes using Cloud Computing
- COPE 1.2.5 - Pair-end Reads Connection tool to facilitate Genome Assembly
- Cortex 1.05.21 - Genome Assembly and Variation Analysis
- crAss v2.2 - Cross-Assembly of Metagenomes
- CSAR / Multi-CSAR - Contig Scaffolding tool using Algebraic Rearrangements
- CStone - de novo Transcriptome Assembler
- Cufflinks 2.2.1 - Transcript Assembler & Abundance Estimator for RNA-Seq
- Curtain 0.2.3 beta - Assembling large Genomes from Short Read Sequences
- Dawg 1.2 - Simulating Sequence Evolution
- DETONATE 1.11 - DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation
- DISCOVAR 51750 - Genome Shotgun Assembler and Variant Caller
- DNA Baser 5.15 - DNA Sequence Assembly & Analysis
- DNA Dragon 1.5.6 build1 - DNA Sequence Contig Assembler Software
- DNPTrapper 1.0 - Assembly Editing & Visualization Tool
- EagleView 2.2 - Genome Assembler Viewer
- EBARDenovo 2.0.1 - Highly-accurate de novo Assembler of Paired-end RNA-Seq
- Edena v3.131028 - De Novo Short Reads Assembler
- ELOPER 1.2 - Elongation of Paired-end Reads for de novo Assembly
- Elviz 2.0 - Exploration of Metagenomic Assemblies
- EPGA2 - De Novo Assembler
- est2assembly 1.13 - Assembly and Annotation of Transcriptomes for any Species
- EvalDNA v1.1 - Evaluation of De Novo Assemblies
- EWRA - Edge-Weighted Reconstruction integrating aDNA Assembly graph
- FASeg 2.0 - Forward Backward Fragment Assembling Segmentation
- FASSI 1.0 - Fingerprint and ASSembly Incorporation
- FastMLST v0.0.15 - Multilocus Sequence Typing of draft Genome Assemblies
- Faucet v0.5 - Streaming de novo Assembly Graph Construction
- Fermi 1.1 - WGS de novo Assembler based on the FMD-index for large Genomes
- FermiKit 0.13 / fermi-lite 0.1- De novo Assembly based Variant Calling pipeline for Illumina Short Reads
- FGAP 1.8.1 - Automated Gap Closing tool
- FinisherSC 2.1 - A Repeat-aware tool for upgrading de-novo Assembly using Long Reads
- FLASH 1.2.11 - Fast Length Adjustment of SHort reads
- FPC 9.4 - Build Contigs from Fingerprinted Clones
- fq2dna 21.06 - FASTQ files to de novo Assembly
- fragScaff - Genome Assembly with Contiguity Preserving Transposition
- FuLinkA 0.5 - Fuzzy Linking Assembler for Genomic Sequences
- GAEMR 1.0.1 - Assembly Analysis Framework
- GAM - Genome Assemblies Merger
- GAM-NGS 1.1b - Genome Assemblies Merger for Next Generation Sequencing
- GAML 0.1 - Genome Assembly by Maximum Likelihood
- GapFiller 2.1.2 - Closing the Gap within Paired Reads
- GeneStitch 1.2.1 - Network Matching Algorithm to Gene Assembly
- Genomix 0.2.11 - Parallel Genome Assembly using Hyracks
- GenSeed 1.0.22 - Seed-driven progressive Assembly program
- GMASS - Genome Assembly Structural Similarity
- GMcloser 1.6.2 / GMvalue 1.3 - Closing the Gaps in Scaffolds with Preassembled Contigs
- GRASP 0.0.4 - Guided Reference-based Assembly of Short Peptides
- GRASS 0.003 - GeneRic ASembly Scaffolder
- GS De Novo Assembler - de novo DNA Sequence Assembly
- hapAssembly - Haplotype Assembly from Whole-Genome Sequence Data
- HapCol 1.1.1 - Haplotype Assembly from Long Gapless Reads
- HapCompass 0.8.2 - A Cycle-Basis Algorithm for Accurate Haplotype Assembly
- HaploClique 1.3.1 - Viral Quasispecies Assembly from Paired-end data
- hapsembler 2.21 - Haplotype-specific Genome Assembly Toolkit
- HASLR - Fast Hybrid Assembly of Long Reads
- HipMer 1.2.2 / MetaHipMer 2.0.1 - Extreme Scale De Novo Genome and MetaGenome Assembler
- HyAsP - Hybrid Assembler for Plasmids
- HyDA 1.3.1 / Squeezambler 2.0.3 - Hybrid De Novo Assembler
- iAssembler 1.3.2 - de novo Assembly of Roche-454/Sanger Transcriptome Sequences
- IDBA / IDBA-UD 1.1.1 - De Bruijn Graph De Novo Assembler with Highly Uneven Sequencing Depth
- IMAGE 2.4.1 - Iterative Mapping and Assembly for Gap Elimination
- IMAP - Chromosome-level Genome Assembler Combining multiple de novo Assemblies
- InteMAP 1.0 - Integrated Metagenomic Assembly pipeline for NGS Short Reads
- IsoLasso 2.6.1 - A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly
- IsoSCM 2.0.12 - Transcript Assembly tool using Multiple Change-point Inference to improve 3'UTR Annotation
- ITMO Genome Assembler 1.6.1
- IVA 1.0.9 - Iterative Virus Assembler
- KARMA 0.9 - Aligner for Mapping Shotgun Sequencer FASTQ Read
- KLEAT 2.0 - Identifies 3' UTR Ends of Transcripts in de novo RNA-Seq Assemblies
- KmerGenie 1.7051 - K-mer size Selection for Genome Assembly
- Kourami v0.9.6 - Graph-guided Assembly for HLA alleles
- LACHESIS - Genome Assembly with Contact Probability Maps
- LaneCheck 0.0.1 - Checking Lane Identity
- LASER - Large genome ASsembly EvaluatoR
- laSV 1.0.2 - Local Assembly based Structural Variation Discovery tool
- LightAssembler - Lightweight Resources Assembly Algorithm
- LongStitch v1.0.1 - Correct and Scaffold Assemblies using long Reads
- Lucy 2.20 - DNA Sequence Quality & Vector Trimming
- MAIA 0.5 - Integrating Genome Assemblies
- MakeHub 1.0.5 - Fully Automated Generation of UCSC Assembly Hubs
- MaLTA - Transcriptome Assembly and Quantification from Ion Torrent RNA-Seq data
- MAP 20121108 - A de novo Metagenomic Assembly program for Shotgun DNA reads
- MaSuRCA 4.0.4 - Whole Genome Short Read Assembler
- MATAM 1.6.0 - Mapping-Assisted Targeted-Assembly for Metagenomics
- MaxBin 2.2.7 - Binning Assembled Metagenomic Sequences
- MAXIMUS 0.2 - Hybrid Reference and de novo Assembly pipeline
- MEGAHIT v1.2.9 - Large and Complex Metagenomics Assembly via Succinct de Bruijn graph
- Meraculous 2.2.6 - De novo Genome Assembler from Short Reads
- Merqury v1.3 - Evaluate Genome Assemblies with k-mers
- MetaCompass 1.0 - Comparative Assembly of Metagenomic Sequences
- MetaCompass v2.0-beta - Reference-guided Assembly of Metagenomes
- MetAMOS 1.5rc3 - Metagenomic Assembly pipeline for AMOS
- MetaPhase - Metagenomic Deconvolution with Hi-C
- MetaProb v2 - Accurate Metagenomic Reads Binning based on Probabilistic Sequence Signatures
- Metassembler 1.5 - Combines multiple Whole Genome de novo Assemblies into a combined Consensus Assembly
- MetaVelvet 1.2.01 / MetaVelvet-SL - An Extension of Velvet Assembler to de novo Metagenomic Assembly / utilizing Supervised Learning
- MindTheGap 2.2.3 - Detection and Assembly of Insertion Variants
- Minia 3.2.6 - Short-read Assembler based on a de Bruijn graph
- miniasm v0.3- Fast Overlapped-based de novo Assembler for Noisy long Reads
- MIRA 4.9.6 - Whole Genome Shotgun and EST Sequence Assembler
- misFinder v0.4.05.05 - Identify Mis-assemblies in an unbiased manner using Reference and Paired-end Reads
- misSEQuel v1.0beta - Misassembly Detection in Draft Genomes
- NanoMark - DNA Assembly Benchmark for Nanopore long reads
- NN50-calculator 0.5 - Evaluate the Correctness of Genome Assemblies
- Novo&Stitch - Genome Assembly Reconciliation tool based on Optical Map
- ntEdit v1.3.5 - Ultra Fast and Scalable Genome Assembly Polishing
- ntJoin v1.0.8 - Genome Assembly Scaffolder using minimizer Graphs
- Oases 0.2.09 - De novo Transcriptome Assembler for very short reads
- Omega 1.0.2 - Overlap-graph de novo Assembler for Metagenomics
- OMWare 1.0 - Efficient Assembly of Genome-wide Physical Maps
- Opera 2.0.6 - Sequence Assembly Program
- PAGIT 1.01 - Post Assembly Genome Improvement Toolkit
- PaKman - Parallel Genome Assembler for Scalable Generation of Genomic Contigs
- PANDASEQ 2.11 / Pandaseq-sam 1.4 - PAired-eND Assembler for DNA sequences
- PASHA 1.0.10 - Parallelized Short Read Assembly
- Pasqual 1.0 - Parallel de Novo Genome Sequence Assembler
- PathRacer 3.15.0 - Racing Profile HMM Paths on Assembly Graph
- PAVFinder v1.7.0 - Post Assembly VariantFinder
- PBSIM 1.0.3 - PacBio Reads Simulator
- PEAR 0.9.8 - Pair-End reads AssembleR
- PEAssember 1.2 - A de novo Genome Assembler
- PERGA 0.5.03.02 - Paired End Reads Guided Assembler
- PGAAS 1.0 - Prokaryotic Genome Assembly Assistant System
- PhrapUMD 2 - Modified version of Phrap
- Phred/Phrap/Consed 29.0 - DNA Sequence Assembler & Finishing Tools
- Phusion 2.1c - Assembly Genome Sequences from Whole Genome Shotgun(WGS) Reads
- pilon v1.24 - Automated Assembly Improvement
- PRICE 1.2 - de novo Genome Assembler
- PsiCLASS 1.0.2 - Reference-based Transcriptome Assembler for Single or Multiple RNA-seq Samples
- PyroCleaner 1.3 - Clean 454 Pyrosequencing Reads in order to ease the Assembly Process
- QSRA 1.0 – Quality-value guided de novo Short Read Assembler
- Quake 0.3.5 - Detect & Correct Substitution Sequencing Errors in WGS Data Sets
- QUAST 5.1.0 - Quality Assessment Tool for Genome Assemblies
- r2cat - Synteny Plots & Comparative Assembly
- RACA - Reference-Assisted Chromosome Assembly
- RaGOO v1.11 - Fast Reference-Guided Scaffolding of Genome Assembly Contigs
- Ragout 2.3 - Tool for Reference-assisted Assembly
- Rainbow v2.0.4 - Clustering and Assembling Short Reads, especially for RAD
- RAMPART 0.12.2 - A Workflow Management System for de novo Genome Assembly
- Ray 2.3.1 - Parallel Genome Assemblies for Parallel DNA sequencing
- RC454 1.2 - Read Alignment and Error Correction tool for Cleaning 454 Reads of Process Errors
- REAGO 1.1 - REconstruct 16S ribosomal RNA Genes from MetagenOmic data
- REAPR 1.0.18 - Genome Assembly Evaluation
- Reconciliator 2.0 - The tool for Merging Assemblies
- rectangles 2.0 - Rectangle Graph for Repeat Resolution in Genome Assembly
- REPdenovo V2 - A tool to Construct Repeats directly from Raw Reads
- rKOMICS 1.1 - Minicircle Sequence Cluster (MSC) Analyses
- RMAP 2.1 - Short-read Mapping
- Rnnotator 3.5.0 - de novo Transcriptome Assembly pipeline from stranded RNA-Seq reads
- SAGE 2 - String Graph Assembly of GEnomes
- SALSA v2.3 - Scaffold long read Assemblies with Hi-C data
- SAM 1.0 - Sequence Assembly Manager
- SAMMate 2.7.4 / assemblySAM 1.1 - Processing Short Read Alignments in SAM/BAM format / RNA-Seq Assembly and Analysis
- SAT-Assembler 20160120 - Scalable and Accurate Targeted Gene Assembly Tool
- SAVAGE 0.4.0 - Strain Aware VirAl GEnome assembly
- Scaffold_builder v2.2 - Order Contigs generated by draft sequencing along a Reference Sequence
- ScaffoldScaffolder 0.1 - Solving Contig Orientation via Bidirected to Directed Graph Reduction
- Scallop v0.10.4 - Reference-based Transcriptome Assembler for RNA-seq
- SCARF - Scaffolded and Corrected Assembly of Roche 454
- scarpa 0.241 - Scaffolding Reads with Practical Algorithms
- SCUBAT - Scaffolding Contigs using BLAT and Transcripts
- SeqAssem 200807- Molecular Sequence Assembly
- SeqCons 2.0.9 - de novo and reference-guided Sequence Assembly
- SEQLandscape v1 - Generation and Visualization of Sequence Landscape
- SEQuel 1.0.2 - Improving the Accuracy of Genome Assemblies
- Sequencher 5.4.6 - DNA Sequence Assembly and Analysis
- SFA-SPA 0.2.1 - A Suffix Array based Short Peptide Assembler for Metagenomic Data
- SGA v0.10.15 - String Graph Assembler
- SHARCGS - SHort read Assembler based on Robust Contig extension for Genome Sequencing
- ShoRAH v1.9.95 - Short Reads Assembly into Haplotypes
- SHORTY 2.0 - de novo Assembler
- SimAssemblyStage1/2 0.2 - Assembly Alignment of Contigs
- SKESA 2.4.0 - Strategic K-mer Extension for Scrupulous Assemblies
- SLICEMBLER - Meta-assembler Designed for Ultra-deep Sequencing data
- SLiQ - Simple linear Inequalities based Mate-Pair reads Filtering and Scaffolding
- SOMA 2.0 - Scaffolding using Optical Restriction Mapping
- SOPRA 1.4.6 - Statistical Optimization of Paired Read Assembly
- SPAdes 3.15.3 - Single-cell Genome Assembler
- Spherical - An iterative approach for Large Metagenome Assemblies
- SR-ASM - DNA Assembly of the Short Sequences coming from 454 sequencer
- SRAssembler v1.0.0 - Selective and Recursive local Assembler
- SSAKE 4.0 - Assembling Millions of short DNA Sequences
- SSP - de novo Transcriptome Assembler
- StriDe - novel Assembler
- SuRankCo R5 - Supervised Ranking of Contigs in de novo Assemblies
- SvABA 1.1.0 - Structural Variation and Indel Detection by local Assembly
- SWALO - Scaffolding with Assembly Likelihood Optimization
- SWAP-Assembler 2 - A scalable and fully parallelized Genome Assembler
- Tablet 1.21.02.08 - Next Generation Sequence Assembly Visualization
- TAG 0.91 - Transcript Assembly by Mapping Reads to Graphs
- Taipan 20090515 - Fast Hybrid Short-read Assembly tool
- TASR 1.6.2 - Targeted Assembly of Sequence Reads
- TCGA-Assembler 2.0.6 - Open-Source Software for Retrieving and Processing TCGA Data
- Tedna 1.3 - Transposable Element De Novo Assembler
- Telescoper 0.2 - De novo Assembly Algorithm
- TGNet - Visualization and Quality Assessment of de novo Genome Assemblies
- THOR 1.0 - Assemble Target Genomic Sequence Orthologs
- TIGER - DNA Sequence Assembly
- Tigmint v1.2.4 - Correct Misassemblies using linked AND long reads
- Tracembler - Contig Assembly Tool
- Trans-ABySS 2.0.1 - Analyze ABySS multi-k-assembled Shotgun Transcriptome Data.
- Transcriptome Assembler - Transcriptome Assembly used in RNA-seq of 16 Mammalian Species
- TransPS 1.1.0 - Transcriptome Post Scaffolding
- treecat - Phylogenetic Comparative Assembly
- TriMetAss 1.2 – The Trinity-based Iterative Metagenomics Assembler
- Trinity 2.13.2 - RNA-Seq De novo Assembly
- TRUST4 v0.1.1 - TCR and BCR Assembly from RNA-seq data
- V-FAT 1.1 - Automated Finishing, Annotation, and QA tool for Viral Assemblies
- VAGUE 1.0.5 - Velvet Assembler Graphical User Environment
- VCAKE 2.0 - Genetic Sequence Assembler
- Velvet 1.2.10 - Sequence Assembler for Very Short Reads
- Velvet-SC 0.7.62 - Velvet modified for Single Cell reads
- VelvetK 20120606 - Find a reasonable K-mer size to Assemble Genome Reads with Velvet
- VelvetOptimiser 2.2.6 - Automatically Optimise Velvet Assembler Parameters
- VICUNA 1.1 - de novo Assembler for Ultra-deep Sequence data
- ViSpA 02 - Viral Spectrum Assembler
- VTBuilder - Assembly of Multi Isoform Transcriptomes
- WEAV 0.2 - de novo Assembly program for both Genome and RNA
- WGA-LP - A Pipeline for Whole Genome Assembly
- WhatsHap - Haplotype Assembly for Future-Generation Sequencing Reads
- Xander - Gene-targeted Metagenomic Assembler
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