List of sequence alignment software
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins.
Database search only
| Name | Description | Sequence Type* | Link | Authors | Year |
|---|---|---|---|---|---|
| BLAST | local search with fast k-tuple heuristic (Basic Local Alignment Search Tool) | Both | NCBI EMBL-EBI DDBJ DDBJ (psi-blast) GenomeNet PIR (protein only) | Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ[1] | 1990 |
| CS-BLAST | sequence-context specific BLAST, more sensitive than BLAST, FASTA, and SSEARCH. Position-specific iterative version CSI-BLAST more sensitive than PSI-BLAST | Protein | CS-BLAST server download | Angermueller C, Biegert A, Soeding J[2] | 2013 |
| CUDASW++ | GPU accelerated Smith Waterman algorithm for multiple shared-host GPUs | Protein | homepage publication | Liu Y, Maskell DL and Schmidt B | 2009/2010 |
| FASTA | local search with fast k-tuple heuristic, slower but more sensitive than BLAST | Both | EMBL-EBI DDBJ GenomeNet PIR (protein only) | ||
| GGSEARCH / GLSEARCH | Global:Global (GG), Global:Local (GL) alignment with statistics | Protein | FASTA server | ||
| HMMER | local and global search with profile Hidden Markov models, more sensitive than PSI-BLAST | Both | download | Durbin R, Eddy SR, Krogh A, Mitchison G[3] | 1998 |
| HHpred / HHsearch | pairwise comparison of profile Hidden Markov models; very sensitive, but can only search alignment databases (Pfam, PDB, InterPro...) | Protein | server download | Söding J[4] | 2005 |
| IDF | Inverse Document Frequency | Both | download | ||
| Infernal | profile SCFG search | RNA | download | Eddy S | |
| KLAST | high-performance general purpose sequence similarity search tool | Both | homepage publication | 2009/2014 | |
| PSI-BLAST | position-specific iterative BLAST, local search with position-specific scoring matrices, much more sensitive than BLAST | Protein | NCBI PSI-BLAST | Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ[5] | 1997 |
| PSI-Search | Combining the Smith-Waterman search algorithm with the PSI-BLAST profile construction strategy to find distantly related protein sequences, and preventing homologous over-extension errors. | Protein | EMBL-EBI PSI-Search | Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR[6] | 2012 |
| ScalaBLAST | Highly parallel Scalable BLAST | Both | ScalaBLAST | Oehmen et al.[7] | 2011 |
| Sequilab | Linking and profiling sequence alignment data from NCBI-BLAST results with major sequence analysis servers/services | Nucleotide/peptide | server | 2010 | |
| SAM | local and global search with profile Hidden Markov models, more sensitive than PSI-BLAST | Both | SAM | Karplus K, Krogh A[8] | 1999 |
| SSEARCH | Smith-Waterman search, slower but more sensitive than FASTA | Both | EMBL-EBI DDBJ | ||
| SWAPHI | the first parallelized algorithm employing the emerging Intel Xeon Phis to accelerate Smith-Waterman protein database search | Protein | homepage | Liu Y and Schmidt B | 2014 |
| SWAPHI-LS | the first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences | DNA | homepage | Liu Y, Tran TT, Lauenroth F, Schmidt B | 2014 |
| SWIPE | fast Smith-Waterman search using SIMD parallelization | Both | homepage | Rognes T | 2011 |
*Sequence Type: Protein or nucleotide
Pairwise alignment
| Name | Description | Sequence Type* | Alignment Type** | Link | Author | Year |
|---|---|---|---|---|---|---|
| ACANA | fast heuristic anchor based pairwise alignment | Both | Both | download | Huang, Umbach, Li | 2005 |
| AlignMe | Alignments for membrane protein sequences | Protein | Both | download,server | M. Stamm, K. Khafizov, R. Staritzbichler, L.R. Forrest | 2013 |
| Bioconductor Biostrings::pairwiseAlignment | Dynamic programming | Both | Both + Ends-free | site | P. Aboyoun | 2008 |
| BioPerl dpAlign | Dynamic programming | Both | Both + Ends-free | site | Y. M. Chan | 2003 |
| BLASTZ,LASTZ | Seeded pattern-matching | Nucleotide | Local | download,download | Schwartz et al.[9][10] | 2004,2009 |
| DNADot | Web-based dot-plot tool | Nucleotide | Global | server | R. Bowen | 1998 |
| DOTLET | Java-based dot-plot tool | Both | Global | applet | M. Pagni and T. Junier | 1998 |
| FEAST | Posterior based local extension with descriptive evolution model | Nucleotide | Local | site | A. K. Hudek and D. G. Brown | 2010 |
| G-PAS | GPU-based dynamic programming with backtracking | Both | Local, SemiGlobal, Global | site+download | W. Frohmberg, M. Kierzynka et al. | 2011 |
| GapMis | GapMis is a tool for pairwise sequence alignment with a single gap | Both | SemiGlobal | site | K. Frousios, T. Flouri, C. S. Iliopoulos, K. Park, S. P. Pissis, G. Tischler | 2012 |
| GGSEARCH, GLSEARCH | Global:Global (GG), Global:Local (GL) alignment with statistics | Protein | Global in query | FASTA server | W. Pearson | 2007 |
| JAligner | Open source Java implementation of Smith-Waterman | Both | Local | JWS | A. Moustafa | 2005 |
| K*Sync | Protein sequence to structure alignment that includes secondary structure, structural conservation, structure-derived sequence profiles, and consensus alignment scores | Protein | Both | Robetta server | D. Chivian & D. Baker [11] | 2003 |
| LALIGN | Multiple, non-overlapping, local similarity (same algorithm as SIM) | Both | Local non-overlapping | server FASTA server | W. Pearson | 1991 (algorithm) |
| NW-align | Standard Needleman-Wunsch dynamic programming algorithm | Protein | Global | server and download | Y Zhang | 2012 |
| mAlign | modelling alignment; models the information content of the sequences | Nucleotide | Both | doc code | D. Powell, L. Allison and T. I. Dix | 2004 |
| matcher | Waterman-Eggert local alignment (based on LALIGN) | Both | Local | Pasteur | I. Longden (modified from W. Pearson) | 1999 |
| MCALIGN2 | explicit models of indel evolution | DNA | Global | server | J. Wang et al. | 2006 |
| MUMmer | suffix tree based | Nucleotide | Global | download | S. Kurtz et al. | 2004 |
| needle | Needleman-Wunsch dynamic programming | Both | SemiGlobal | EMBL-EBIPasteur | A. Bleasby | 1999 |
| Ngila | logarithmic and affine gap costs and explicit models of indel evolution | Both | Global | download | R. Cartwright | 2007 |
| Path | Smith-Waterman on protein back-translation graph (detects frameshifts at protein level) | Protein | Local | server download | M. Gîrdea et al.[12] | 2009 |
| PatternHunter | Seeded pattern-matching | Nucleotide | Local | download | B. Ma et al.[13][14] | 2002–2004 |
| ProbA (also propA) | Stochastic partition function sampling via dynamic programming | Both | Global | download | U. Mückstein | 2002 |
| PyMOL | "align" command aligns sequence & applies it to structure | Protein | Global (by selection) | site | W. L. DeLano | 2007 |
| REPuter | suffix tree based | Nucleotide | Local | download | S. Kurtz et al. | 2001 |
| SABERTOOTH | Alignment using predicted Connectivity Profiles | Protein | Global | download on request | F. Teichert, J. Minning, U. Bastolla, and M. Porto | 2009 |
| Satsuma | Parallel whole-genome synteny alignments | DNA | Local | download | M.G. Grabherr et al. | 2010 |
| SEQALN | Various dynamic programming | Both | Local or Global | server | M.S. Waterman and P. Hardy | 1996 |
| SIM, GAP, NAP, LAP | Local similarity with varying gap treatments | Both | Local or global | server | X. Huang and W. Miller | 1990-6 |
| SIM | Local similarity | Both | Local | servers | X. Huang and W. Miller | 1991 |
| SPA: Super pairwise alignment | Fast pairwise global alignment | Nucleotide | Global | available upon request | Shen, Yang, Yao, Hwang | 2002 |
| SSEARCH | Local (Smith-Waterman) alignment with statistics | Protein | Local | EMBL-EBI FASTA server | W. Pearson | 1981 (Algorithm) |
| Sequences Studio | Java applet demonstrating various algorithms from [15] | Generic sequence | Local and global | code applet | A.Meskauskas | 1997 (reference book) |
| SWIFT suit | Fast Local Alignment Searching | DNA | Local | site | K. Rasmussen,[16] W. Gerlach | 2005,2008 |
| stretcher | Memory-optimized Needleman-Wunsch dynamic programming | Both | Global | Pasteur | I. Longden (modified from G. Myers and W. Miller) | 1999 |
| tranalign | Aligns nucleic acid sequences given a protein alignment | Nucleotide | NA | Pasteur | G. Williams (modified from B. Pearson) | 2002 |
| UGENE | Opensource Smith-Waterman for SSE/CUDA, Suffix array based repeats finder & dotplot | Both | Both | UGENE site | UniPro | 2010 |
| water | Smith-Waterman dynamic programming | Both | Local | EMBL-EBIPasteur | A. Bleasby | 1999 |
| wordmatch | k-tuple pairwise match | Both | NA | Pasteur | I. Longden | 1998 |
| YASS | Seeded pattern-matching | Nucleotide | Local | server download | L. Noe and G. Kucherov [17] | 2004–2011 |
*Sequence Type: Protein or nucleotide. **Alignment Type: Local or global
Multiple sequence alignment
| Name | Description | Sequence Type* | Alignment Type** | Link | Author | Year | License |
|---|---|---|---|---|---|---|---|
| ABA | A-Bruijn alignment | Protein | Global | download | B.Raphael et al. | 2004 | Proprietary, without charge for educational, research and non profit. |
| ALE | manual alignment ; some software assistance | Nucleotides | Local | download | J. Blandy and K. Fogel | 1994 (latest version 2007) | GPL2 |
| AMAP | Sequence annealing | Both | Global | server | A. Schwartz and L. Pachter | 2006 | |
| anon. | fast, optimal alignment of three sequences using linear gap costs | Nucleotides | Global | paper software | D. Powell, L. Allison and T. I. Dix | 2000 | |
| BAli-Phy | Tree+Multi alignment ; Probabilistic/Bayesian ; Joint Estimation | Both | Global | WWW+download | BD Redelings and MA Suchard | 2005 (latest version 2015) | GPL |
| Base-By-Base | Java-based multiple sequence alignment editor with integrated analysis tools | Both | Local or Global | download | R. Brodie et al. | 2004 | Free, requires registration. |
| CHAOS/DIALIGN | Iterative alignment | Both | Local (preferred) | server | M. Brudno and B. Morgenstern | 2003 | |
| ClustalW | Progressive alignment | Both | Local or Global | download EMBL-EBI DDBJ PBIL EMBNet GenomeNet | Thompson et al. | 1994 | GNU Lesser GPL |
| CodonCode Aligner | Multi alignment; ClustalW & Phrap support | Nucleotides | Local or Global | download | P. Richterich et al. | 2003 (latest version 2009) | |
| Compass | COmparison of Multiple Protein sequence Alignments with assessment of Statistical Significance | Protein | Global | download and server | R.I. Sadreyev, et al. | 2009 | |
| DECIPHER | Progressive/iterative alignment | Both | Global | download | Erik S. Wright | 2014 | GPL |
| DIALIGN-TX and DIALIGN-T | Segment-based method | Both | Local (preferred) or Global | download and server | A.R.Subramanian | 2005 (latest version 2008) | |
| DNA Alignment | Segment-based method for intraspecific alignments | Both | Local (preferred) or Global | server | A.Roehl | 2005 (latest version 2008) | |
| DNA Baser Sequence Assembler | Multi alignment; Automatic batch alignment | Nucleotides | Local or Global | www.DnaBaser.com | Heracle BioSoft | 2006 (latest version 2014) | |
| EDNA | Energy Based Multiple Sequence Alignment for DNA Binding Sites | Nucleotides | Local or Global | sourceforge.net/projects/msa-edna/ | Salama, RA. et al. | 2013 | |
| FSA | Sequence annealing | Both | Global | download and server | R. K. Bradley et al. | 2008 | |
| Geneious | Progressive/Iterative alignment; ClustalW plugin | Both | Local or Global | download | A.J. Drummond et al. | 2005 (latest version 2009) | |
| Kalign | Progressive alignment | Both | Global | serverEMBL-EBI MPItoolkit | T. Lassmann | 2005 | |
| MAFFT | Progressive/iterative alignment | Both | Local or Global | GenomeNet MAFFT | K. Katoh et al. | 2005 | |
| MARNA | Multiple Alignment of RNAs | RNA | Local | server download | S. Siebert et al. | 2005 | |
| MAVID | Progressive alignment | Both | Global | server | N. Bray and L. Pachter | 2004 | |
| MSA | Dynamic programming | Both | Local or Global | download | D.J. Lipman et al. | 1989 (modified 1995) | |
| MSAProbs | Dynamic programming | Protein | Global | download | Y. Liu, B. Schmidt, D. Maskell | 2010 | |
| MULTALIN | Dynamic programming/clustering | Both | Local or Global | server download | F. Corpet | 1988 | |
| Multi-LAGAN | Progressive dynamic programming alignment | Both | Global | server | M. Brudno et al. | 2003 | |
| MUSCLE | Progressive/iterative alignment | Both | Local or Global | server | R. Edgar | 2004 | |
| Opal | Progressive/iterative alignment | Both | Local or Global | download | T. Wheeler and J. Kececioglu | 2007 | |
| Pecan | Probabilistic/consistency | DNA | Global | download | B. Paten et al. | 2008 | |
| Phylo | A human computing framework for comparative genomics to solve multiple alignment | Nucleotides | Local or Global | site | McGill Bioinformatics | 2010 | |
| Praline | Progressive/iterative/consistency/homology-extended alignment with pre-profiling and secondary structure prediction | Protein | Global | server | J. Heringa | 1999 (latest version 2009) | |
| PicXAA | non-progressive/maximum expected accuracy alignment | Both | Global | download and server | S.M.E. Sahraeian and B.J. Yoon | 2010 | |
| POA | Partial order/hidden Markov model | Protein | Local or Global | download | C. Lee | 2002 | |
| Probalign | Probabilistic/consistency with partition function probabilities | Protein | Global | server | Roshan and Livesay | 2006 | |
| ProbCons | Probabilistic/consistency | Protein | Local or Global | server | C. Do et al. | 2005 | |
| PROMALS3D | Progressive alignment/hidden Markov model/Secondary structure/3D structure | Protein | Global | server | J. Pei et al. | 2008 | |
| PRRN/PRRP | Iterative alignment (especially refinement) | Protein | Local or Global | PRRP PRRN | Y. Totoki (based on O. Gotoh) | 1991 and later | |
| PSAlign | Alignment preserving non-heuristic | Both | Local or Global | download | S.H. Sze, Y. Lu, Q. Yang. | 2006 | |
| RevTrans | Combines DNA and Protein alignment, by back translating the protein alignment to DNA. | DNA/Protein (special) | Local or Global | server | Wernersson and Pedersen | 2003 (newest version 2005) | |
| SAGA | Sequence alignment by genetic algorithm | Protein | Local or Global | download | C. Notredame et al. | 1996 (new version 1998) | |
| SAM | Hidden Markov model | Protein | Local or Global | server | A. Krogh et al. | 1994 (most recent version 2002) | |
| Se-Al | Manual alignment | Both | Local | download | A. Rambaut | 2002 | |
| StatAlign | Bayesian co-estimation of alignment and phylogeny (MCMC) | Both | Global | download | A. Novak et al. | 2008 | |
| Stemloc | Multiple alignment and secondary structure prediction | RNA | Local or Global | download | I. Holmes | 2005 | GPLv3 (parte de DART) |
| T-Coffee | More sensitive progressive alignment | Both | Local or Global | server download | C. Notredame et al. | 2000 (newest version 2008) | GPL2 |
| UGENE | Supports multiple alignment with MUSCLE, KAlign, Clustal and MAFFT plugins | Both | Local or Global | download | UGENE team | 2010 (newest version 2012) | GPL2 |
| VectorFriends | VectorFriends Aligner, MUSCLE plugin, and ClustalW plugin | Both | Local or Global | download | BioFriends team | 2013 | Proprietary, but free for academic researchers |
| GLProbs | Adaptive pair-Hidden Markov Model based approach | Protein | Global | download | Y. Ye et al. | 2013 |
*Sequence Type: Protein or nucleotide. **Alignment Type: Local or global
Genomics analysis
| Name | Description | Sequence Type* | Link |
|---|---|---|---|
| ACT (Artemis Comparison Tool) | Synteny and comparative genomics | Nucleotide | server |
| AVID | Pairwise global alignment with whole genomes | Nucleotide | server |
| BLAT | Alignment of cDNA sequences to a genome. | Nucleotide | [18] |
| GMAP | Alignment of cDNA sequences to a genome. Identifies splice site junctions with high accuracy. | Nucleotide | http://research-pub.gene.com/gmap |
| Splign | Alignment of cDNA sequences to a genome. Identifies splice site junctions with high accuracy. Able to recognize and separate gene duplications. | Nucleotide | http://www.ncbi.nlm.nih.gov/sutils/splign |
| Mauve | Multiple alignment of rearranged genomes (also available inside Geneious) | Nucleotide | download |
| MGA | Multiple Genome Aligner | Nucleotide | download |
| Mulan | Local multiple alignments of genome-length sequences | Nucleotide | server |
| Multiz | Multiple alignment of genomes | Nucleotide | download |
| PLAST-ncRNA | Search for ncRNAs in genomes by partition function local alignment | Nucleotide | server |
| Sequerome | Profiling sequence alignment data with major servers/services | Nucleotide/peptide | server |
| Sequilab | Profiling sequence alignment data from NCBI-BLAST results with major servers/services | Nucleotide/peptide | server |
| Shuffle-LAGAN | Pairwise glocal alignment of completed genome regions | Nucleotide | server |
| SIBsim4 / Sim4 | A program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns | Nucleotide | download |
| SLAM | Gene finding, alignment, annotation (human-mouse homology identification) | Nucleotide | server |
*Sequence Type: Protein or nucleotide
Motif finding
| Name | Description | Sequence Type* | Link |
|---|---|---|---|
| PMS | Motif search and discovery | Both | server server |
| FMM | Motif search and discovery (can get also positive & negative sequences as input for enriched motif search) | Nucleotide | server |
| BLOCKS | Ungapped motif identification from BLOCKS database | Both | server |
| eMOTIF | Extraction and identification of shorter motifs | Both | servers |
| Gibbs motif sampler | Stochastic motif extraction by statistical likelihood | Both | server server |
| HMMTOP | Prediction of transmembrane helices and topology of proteins | Protein | homepage & download |
| I-sites | Local structure motif library | Protein | server |
| JCoils | Prediction of Coiled coil and Leucine Zipper | Protein | homepage & download |
| MEME/MAST | Motif discovery and search | Both | server |
| CUDA-MEME | GPU accelerated MEME (v4.4.0) algorithm for GPU clusters | Both | homepage |
| MERCI | Discriminative motif discovery and search | Both | homepage & download |
| PHI-Blast | Motif search and alignment tool | Both | Pasteur |
| Phyloscan | Motif search tool | Nucleotide | server |
| PRATT | Pattern generation for use with ScanProsite | Protein | server |
| ScanProsite | Motif database search tool | Protein | server |
| TEIRESIAS | Motif extraction and database search | Both | server |
| BASALT | Multiple motif and regular expression search | Both | homepage |
*Sequence Type: Protein or nucleotide
Benchmarking
| Name | Link | Authors |
|---|---|---|
| BAliBASE | download | Thompson, Plewniak, Poch |
| HOMSTRAD | download | Mizuguchi |
| Oxbench | download | Raghava, Searle, Audley, Barber, Barton |
| PFAM | download | |
| PREFAB | download | Edgar |
| SABmark | download | Van Walle, Lasters, Wyns |
| SMART | download | Letunic, Copley, Schmidt, Ciccarelli, Doerks, Schultz, Ponting, Bork |
Alignment Viewers/Editors
Please see the List of alignment visualization software.
Short-Read Sequence Alignment
| Name | Description | paired-end option | Use FASTQ quality | Gapped | Multi-threaded | License | Link | Reference | Year |
|---|---|---|---|---|---|---|---|---|---|
| BarraCUDA | A GPGPU accelerated Burrows-Wheeler transform (FM-index) short read alignment program based on BWA, supports alignment of indels with gap openings and extensions. | Yes | No | Yes | Yes (POSIX Threads and CUDA) | GPL | link | ||
| BBMap | Uses a short kmers to rapidly index genome; no size or scaffold count limit. Higher sensitivity and specificity than Burrows-Wheeler aligners, with similar or greater speed. Performs affine-transform-optimized global alignment, which is slower but more accurate than Smith-Waterman. Handles Illumina, 454, PacBio, Sanger, and Ion Torrent data. Splice-aware; capable of processing long indels and RNA-seq. Pure Java; runs on any platform. Used by the Joint Genome Institute. | Yes | Yes | Yes | Yes | BSD | link | 2010 | |
| BFAST | Explicit time and accuracy tradeoff with a prior accuracy estimation, supported by indexing the reference sequences. Optimally compresses indexes. Can handle billions of short reads. Can handle insertions, deletions, SNPs, and color errors (can map ABI SOLiD color space reads). Performs a full Smith Waterman alignment. | Yes (POSIX Threads) | GPL | link | [19] | 2009 | |||
| BLASTN | BLAST's nucleotide alignment program, slow and not accurate for short reads, and uses a sequence database (EST, sanger sequence) rather than a reference genome. | link | |||||||
| BLAT | Made by Jim Kent. Can handle one mismatch in initial alignment step. | Yes (client/server). | Free for academic and non-commercial use. | link | [20] | 2002 | |||
| Bowtie | Uses a Burrows-Wheeler transform to create a permanent, reusable index of the genome; 1.3 GB memory footprint for human genome. Aligns more than 25 million Illumina reads in 1 CPU hour. Supports Maq-like and SOAP-like alignment policies | Yes | Yes | No | Yes (POSIX Threads) | Artistic License | link | [21] | 2009 |
| HIVE-hexagon | Uses a hash table and bloom matrix to create and filter potential positions on the genome. For higher efficiency uses cross-similarity between short reads and avoids realigning non unique redundant sequences. It is faster than bowtie and bwa and allows indels and divergent sensitive alignments on viruses and bacteria as well as more conservative eukaryotic alignments. | Yes | Yes | Yes | Yes | Free for academic and non-commercial users registered to HIVE deployment instance. | link | [22] | 2014 |
| BWA | Uses a Burrows-Wheeler transform to create an index of the genome. It's a bit slower than bowtie but allows indels in alignment. | Yes | No | Yes | Yes | GPL | link | [23] | 2009 |
| BWA-PSSM | A probabilistic short read aligner based on the use of position specific scoring matrices (PSSM). The aligner is adaptable in the sense that it can take into account the quality scores of the reads and models of data specific biases, such as those observed in Ancient DNA, PAR-CLIP data or genomes with biased nucleotide compositions.[24] | Yes | Yes | Yes | Yes | GPL | link | [24] | 2014 |
| CASHX | Quantify and manage large quantities of short-read sequence data. CASHX pipeline contains a set of tools that can be used together or as independent modules on their own. This algorithm is very accurate for perfect hits to a reference genome. | No | Free for academic and non-commercial use. | link | |||||
| Cloudburst | Short-read mapping using Hadoop MapReduce | Yes (Hadoop MapReduce) | Artistic License | link | |||||
| CUDA-EC | Short-read alignment error correction using GPUs. | Yes (GPU enabled) | link- | ||||||
| CUSHAW | A CUDA compatible short read aligner to large genomes based on Burrows-Wheeler transform. | Yes | Yes | No | Yes (GPU enabled) | GPL | link | [25] | 2012 |
| CUSHAW2 | Gapped short-read and long-read alignment based on maximal exact match seeds. This aligner supports both base-space (e.g. from Illumina, 454, Ion Torrent and PacBio sequencers) and ABI SOLiD color-space read alignments. | Yes | No | Yes | Yes | GPL | link | 2014 | |
| CUSHAW2-GPU | GPU-accelerated CUSHAW2 short-read aligner. | Yes | No | Yes | Yes | GPL | link | ||
| CUSHAW3 | Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding | Yes | No | Yes | Yes | GPL | link | [26] | 2012 |
| drFAST | Read mapping alignment software that implements cache obliviousness to minimize main/cache memory transfers like mrFAST and mrsFAST, however designed for the SOLiD sequencing platform (color space reads). It also returns all possible map locations for improved structural variation discovery. | Yes | Yes (for structural variation) | Yes | No | BSD | link | ||
| ELAND | Implemented by Illumina. Includes ungapped alignment with a finite read length. | ||||||||
| ERNE | Extended Randomized Numerical alignEr for accurate alignment of NGS reads. It can map bisulfite-treated reads. | Yes | Low quality bases trimming | Yes | Multithreading and MPI-enabled | GPL v3 | link | ||
| GASSST | Finds global alignments of short DNA sequences against large DNA banks | Multithreading | CeCILL version 2 License. | link | [27] | 2011 | |||
| GEM | High-quality alignment engine (exhaustive mapping with substitutions and indels). More accurate and several times faster than BWA or Bowtie 1/2. Many standalone biological applications (mapper, split mapper, mappability, and other) provided. | Yes | Yes | Yes | Yes | Dual (free for non-commercial use); GEM source is currently unavailable | link | [28] | 2012 |
| Genalice MAP | Ultra fast and comprehensive NGS read aligner with high precision and small storage footprint. | Yes | Low quality bases trimming | Yes | Yes | Commercial | link | ||
| Geneious Assembler | Fast, accurate overlap assembler with the ability to handle any combination of sequencing technology, read length, any pairing orientations, with any spacer size for the pairing, with or without a reference genome. | Yes | Commercial | link | |||||
| GensearchNGS | Complete framework with user-friendly GUI to analyse NGS data. It integrates a proprietary high quality alignment algorithm as well as plug-in capability to integrate various public aligner into a framework allowing to import short reads, align them, detect variants and generate reports. It is geared towards re-sequencing projects, namely in a diagnostic setting. | Yes | No | Yes | Yes | Commercial | link | ||
| GMAP and GSNAP | Robust, fast short-read alignment. GMAP: longer reads, with multiple indels and splices (see entry above under Genomics analysis); GSNAP: shorter reads, with a single indel or up to two splices per read. Useful for digital gene expression, SNP and indel genotyping. Developed by Thomas Wu at Genentech. Used by the National Center for Genome Resources (NCGR) in Alpheus. | Yes | Yes | Yes | Yes | Free for academic and non-commercial use. | link | ||
| GNUMAP | Accurately performs gapped alignment of sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. Includes adaptor trimming, SNP calling and Bisulfite sequence analysis. | Yes (also supports Illumina *_int.txt and *_prb.txt files with all 4 quality scores for each base) | Multithreading and MPI-enabled | link | [29] | 2009 | |||
| iSAAC | iSAAC has been designed to take full advantage of all the computational power available on a single server node. As a result iSAAC scales well over a broad range of hardware architectures, and alignment performance improves with hardware capabilities | Yes | Yes | Yes | Yes | BSD | github | ||
| LAST | LAST uses adaptative seeds and copes more efficiently with repeat-rich sequences (e.g. genomes). For example: it can align reads to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. | Yes | Yes | Yes | No | GPL | link | [30] | 2011 |
| MAQ | Ungapped alignment that takes into account quality scores for each base. | GPL | link | ||||||
| mrFAST and mrsFAST | Gapped (mrFAST) and ungapped (mrsFAST) alignment software that implements cache obliviousness to minimize main/cache memory transfers. They are designed for the Illumina sequencing platform and they can return all possible map locations for improved structural variation discovery. | Yes | Yes (for structural variation) | Yes | No | BSD | mrFAST mrsFAST | ||
| MOM | MOM or maximum oligonucleotide mapping is a query matching tool that captures a maximal length match within the short read. | Yes | link | ||||||
| MOSAIK | Fast gapped aligner and reference-guided assembler. Aligns reads using a banded Smith-Waterman algorithm seeded by results from a k-mer hashing scheme. Supports reads ranging in size from very short to very long. | Yes | link | ||||||
| MPscan | Fast aligner based on a filtration strategy (no indexing, use q-grams and Backward Nondeterministic DAWG Matching) | link | [31] | 2009 | |||||
| Novoalign & NovoalignCS | Gapped alignment of single end and paired end Illumina GA I & II, ABI Colour space & ION Torrent reads.. High sensitivity and specificity, using base qualities at all steps in the alignment. Includes adapter trimming, base quality calibration, Bi-Seq alignment, and option to report multiple alignments per read. | Yes | Yes | Yes | Multi-threading and MPI versions available with paid license. | Single threaded version free for academic and non-commercial use. | Novocraft | ||
| NextGENe | NextGENe® software has been developed specifically for use by biologists performing analysis of next generation sequencing data from Roche Genome Sequencer FLX, Illumina GA/HiSeq, Life Technologies Applied BioSystems’ SOLiD™ System, PacBio and Ion Torrent platforms. | Yes | Yes | Yes | Yes | Commercial | Softgenetics | ||
| NextGenMap | Flexible and fast read mapping program (twice as fast as BWA), achieves a mapping sensitivity comparable to Stampy. Internally uses a memory efficient index structure (hash table) to store the positions of all 13-mers present in the reference genome. Mapping regions where pairwise alignments are required are dynamically determined for each read. Uses fast SIMD instructions (SSE) to accelerate the alignment calculations on the CPU. If available, alignments are computed on the GPU (using OpenCL/CUDA) resulting in an additional runtime reduction of 20 - 50%. | Yes | No | Yes | Yes (POSIX Threads, OpenCL/CUDA, SSE) | Open Source | Official GitHub Page | [32] | 2013 |
| Omixon | The Omixon Variant Toolkit includes highly sensitive and highly accurate tools for detecting SNPs and indels. It offers a solution to map NGS short reads with a moderate distance (up to 30% sequence divergence) from reference genomes. It poses no restrictions on the size of the reference, which, combined with its high sensitivity, makes the Variant Toolkit well-suited for targeted sequencing projects and diagnostics. | Yes | Yes | Yes | Yes | Commercial | www.omixon.com | ||
| PALMapper | PALMapper, efficiently computes both spliced and unspliced alignments at high accuracy. Relying on a machine learning strategy combined with a fast mapping based on a banded Smith-Waterman-like algorithm it aligns around 7 million reads per hour on a single CPU. It refines the originally proposed QPALMA approach. | Yes | GPL | link | |||||
| Partek | Partek® Flow software has been developed specifically for use by biologists and bioinformaticians. It supports un-gapped, gapped and splice-junction alignment from single and paired-end reads from Illumina, Life technologies Solid TM, Roche 454 and Ion Torrent raw data (with or without quality information). It integrates powerful quality control on FASTQ/Qual level and on aligned data. Additional functionality include trimming and filtering of raw reads, SNP and InDel detection, mRNA and microRNA quantification and fusion gene detection. | Yes | Yes | Yes | Multiprocessor/Core, Client-Server installation possible | Commercial, FREE trial version | |||
| PASS | Indexes the genome, then extends seeds using pre-computed alignments of words. Works with base space as well as color space (SOLID) and can align genomic and spliced RNA-seq reads. | Yes | Yes | Yes | Yes | Free for academic and non-commercial use. | PASS_HOME | ||
| PerM | Indexes the genome with periodic seeds to quickly find alignments with full sensitivity up to four mismatches. It can map Illumina and SOLiD reads. Unlike most mapping programs, speed increases for longer read lengths. | Yes | GPL | link | [33] | ||||
| PRIMEX | Indexes the genome with a k-mer lookup table with full sensitivity up to an adjustable number of mismatches. It is best for mapping 15-60bp sequences to a genome. | No | No | Yes | No (multiple processes per search) | link | 2003 | ||
| QPalma | Is able to take advantage of quality scores, intron lengths and computation splice site predictions to perform and performs an unbiased alignment. Can be trained to the specifics of a RNA-seq experiment and genome. Useful for splice site/intron discovery and for gene model building. (See PALMapper for a faster version). | Yes (client/server) | GPLv2 | link | |||||
| RazerS | No read length limit. Hamming or edit distance mapping with configurable error rates. Configurable and predictable sensitivity (runtime/sensitivity tradeoff). Supports paired-end read mapping. | LGPL | link | ||||||
| REAL, cREAL | REAL is an efficient, accurate, and sensitive tool for aligning short reads obtained from next-generation sequencing. The programme can handle an enormous amount of single-end reads generated by the next-generation Illumina/Solexa Genome Analyzer. cREAL is a simple extension of REAL for aligning short reads obtained from next-generation sequencing to a genome with circular structure. | Yes | Yes | GPL | link | ||||
| RMAP | Can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated read mapping. There are no limitations on read length or number of mismatches. | Yes | Yes | Yes | GPL v3 | link | |||
| rNA | A randomized Numerical Aligner for Accurate alignment of NGS reads | Yes | Low quality bases trimming | Yes | Multithreading and MPI-enabled | GPL v3 | link | ||
| RTG Investigator | Extremely fast, tolerant to high indel and substitution counts. Includes full read alignment. Product includes comprehensive pipelines for variant detection and metagenomic analysis with any combination of Illumina, Complete Genomics and Roche 454 data. | Yes | Yes, for variant calling | Yes | Yes | Free for individual investigator use. | link | ||
| Segemehl | Can handle insertions, deletions and mismatches. Uses enhanced suffix arrays. | Yes | No | Yes | Yes | Free for non-commercial use | link | [34] | 2009 |
| SeqMap | Up to 5 mixed substitutions and insertions/deletions. Various tuning options and input/output formats. | Free for academic and non-commercial use. | link | ||||||
| Shrec | Short read error correction with a Suffix trie data structure. | Yes (Java) | link | ||||||
| SHRiMP | Indexes the reference genome as of version 2. Uses masks to generate possible keys. Can map ABI SOLiD color space reads. | Yes | Yes | Yes | Yes (OpenMP) | BSD derivative | link | 2009 - 2011 | |
| SLIDER | Slider is an application for the Illumina Sequence Analyzer output that uses the "probability" files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. | link | |||||||
| SOAP, SOAP2, SOAP3 and SOAP3-dp | SOAP: Robust with a small (1-3) number of gaps and mismatches. Speed improvement over BLAT, uses a 12 letter hash table. SOAP2: using bidirectional BWT to build the index of reference, and it is much faster than the first version. SOAP3: GPU-accelerated version that could find all 4-mismatch alignments in tens of seconds per one million reads. SOAP3-dp, also GPU accelerated, supports arbitrary number of mismatches and gaps according to affine gap penalty scores. | Yes | No | SOAP3-dp:Yes | Yes (POSIX Threads), SOAP3, SOAP3-dp need GPU with CUDA support. | GPL | link | [37][38] | |
| SOCS | For ABI SOLiD technologies. Significant increase in time to map reads with mismatches (or color errors). Uses an iterative version of the Rabin-Karp string search algorithm. | Yes | GPL | link | |||||
| SSAHA and SSAHA2 | Fast for a small number of variants. | Free for academic and non-commercial use. | link | ||||||
| Stampy | For Illumina reads. High specificity, and sensitive for reads with indels, structural variants, or many SNPs. Slow, but speed increased dramatically by using BWA for first alignment pass). | Yes | Yes | Yes | No | Free for academic and non-commercial use | link | [39] | 2010 |
| SToRM | For Illumina or ABI SOLiD reads, with SAM native output. Highly sensitive for reads with many errors, indels (full from 0 to 15, extended support otherwise). Uses spaced seeds (single hit) and a very fast SSE/SSE2/AVX2/AVX-512 banded alignment filter. For fixed-length reads only, authors recommend SHRiMP2 otherwise. | No | Yes | Yes | Yes (OpenMP) | Open source | link | [40] | 2010 |
| Subread and Subjunc | Superfast and accurate read aligners. Subread can be used to map both gDNA-seq and RNA-seq reads. Subjunc detects exon-exon junctions and maps RNA-seq reads. They employ a novel mapping paradigm called "seed-and-vote". | Yes | Yes | Yes | Yes | GPL3 | link link | ||
| Taipan | de-novo Assembler for Illumina reads | Free for academic and non-commercial use. | link | ||||||
| UGENE | Visual interface both for Bowtie and BWA, as well as an embedded aligner | Yes | Yes | Yes | Yes | Opensource, GPL | link | ||
| VelociMapper | FPGA-accelerated reference sequence alignment mapping tool from TimeLogic. Faster than Burrows-Wheeler transform-based algorithms like BWA and Bowtie. Supports up to 7 mismatches and/or indels with no performance penalty. Produces sensitive Smith-Waterman gapped alignments. | Yes | Yes | Yes | Yes | Commercial | TimeLogic | ||
| XpressAlign | FPGA based sliding window short read aligner which exploits the embarrassingly parallel property of short read alignment. Performance scales linearly with number of transistors on a chip (i.e. performance guaranteed to double with each iteration of Moore's Law without modification to algorithm). Low power consumption is useful for datacentre equipment. Predictable runtime. Better price/performance than software sliding window aligners on current hardware, but not better than software BWT-based aligners currently. Can cope with large numbers (>2) of mismatches. Will find all hit positions for all seeds. Single-FPGA experimental version, needs work to develop it into a multi-FPGA production version. | Free for academic and non-commercial use. | link | ||||||
| ZOOM | 100% sensitivity for a reads between 15 - 240bp with practical mismatches. Very fast. Support insertions and deletions. Works with Illumina & SOLiD instruments, not 454. | Yes (GUI) No (CLI). | Commercial | link | [41] |
See also
- List of open source bioinformatics software
References
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- ↑ Sedlazeck, Fritz J.; Rescheneder, Philipp; von Haeseler, Arndt (2013). "NextGenMap: fast and accurate read mapping in highly polymorphic genomes". Bioinformatics 29 (21): 2790–2791. doi:10.1093/bioinformatics/btt468. PMID 23975764.
- ↑ Chen, Yangho; Souaiaia, Tade; Chen, Ting (2009). "PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds". Bioinformatics 25 (19): 2514–2521. doi:10.1093/bioinformatics/btp486. PMC 2752623. PMID 19675096.
- ↑ Searls, David B.; Hoffmann, Steve; Otto, Christian; Kurtz, Stefan; Sharma, Cynthia M.; Khaitovich, Philipp; Vogel, Jörg; Stadler, Peter F.; Hackermüller, Jörg (2009). "Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures". PLoS Computational Biology 5 (9): e1000502. doi:10.1371/journal.pcbi.1000502. ISSN 1553-7358. PMC 2730575. PMID 19750212.
- ↑ Rumble, Stephen M.; Lacroute, Phil; Dalca, Adrian V.; Fiume, Marc; Sidow, Arend; Brudno, Michael (2009). "SHRiMP: Accurate Mapping of Short Color-space Reads". PLOS Computational Biology 5 (5): e1000386. doi:10.1371/journal.pcbi.1000386. PMC 2678294. PMID 19461883.
- ↑ David, Matei; Dzamba, Misko; Lister, Dan; Ilie, Lucian; Brudno, Michael (2011). "SHRiMP2: Sensitive yet Practical Short Read Mapping". Bioinformatics 27 (7): 1011–1012. doi:10.1093/bioinformatics/btr046. PMID 21278192.
- ↑ Li, R.; Li, Y.; Kristiansen, K.; Wang, J. (2008). "SOAP: short oligonucleotide alignment program". Bioinformatics 24 (5): 713–714. doi:10.1093/bioinformatics/btn025. ISSN 1367-4803. PMID 18227114.
- ↑ Li, R.; Yu, C.; Li, Y.; Lam, T.-W.; Yiu, S.-M.; Kristiansen, K.; Wang, J. (2009). "SOAP2: an improved ultrafast tool for short read alignment". Bioinformatics 25 (15): 1966–1967. doi:10.1093/bioinformatics/btp336. ISSN 1367-4803. PMID 19497933.
- ↑ Lunter, G.; Goodson, M. (2010). "Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads". Genome Research 21 (6): 936–939. doi:10.1101/gr.111120.110. ISSN 1088-9051. PMID 20980556.
- ↑ Noe, L.; Girdea, M.; Kucherov, G. (2010). "Designing efficient spaced seeds for SOLiD read mapping". Advances in Bioinformatics 2010: 708501. doi:10.1155/2010/708501. PMC 2945724. PMID 20936175.
- ↑ Lin, H.; Zhang, Z.; Zhang, M.Q.; Ma, B.; Li, M. (2008). "ZOOM! Zillions of oligos mapped". Bioinformatics 24 (21): 2431–2437. doi:10.1093/bioinformatics/btn416. PMC 2732274. PMID 18684737.
External links
- Pollard, Daniel A; Bergman, Casey M; Stoye, Jens; Celniker, Susan E; Eisen, Michael B (2004). "Benchmarking tools for the alignment of functional noncoding DNA". BMC Bioinformatics 5: 6. doi:10.1186/1471-2105-5-6. PMC 344529. PMID 14736341.: The authors discuss LAGAN, CHAOS, and Dialign as the most effective tools tested for certain uses.