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.
Contents[hide] |
Name | Description | Sequence Type* | Link | Authors | Year |
---|---|---|---|---|---|
BLAST | local search with fast k-tuple heuristic (Basic Local Alignment Search Tool) | Both | NCBI EBI DDBJ DDBJ (psi-blast) GenomeNet PIR (protein on | Myers E, Altschul SF, Gish W, Miller EW, Lipman DJ, NCBI | 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 | Biegert A and S?ding J | 2009 |
FASTA | local search with fast k-tuple heuristic, slower but more sensitive than BLAST | Both | EBI DDBJ GenomeNet PIR (protein on | ||
GGSEARCH / GLSEARCH | Global:Global (GG), Global:Local (GL) alignment with statistics | Protein | FASTA server | ||
HMMER | local and global search with pro | Both | download DDBJ (HMMPFAM) | Eddy SR, Krogh A, Mitchison G | 1998 |
HHpred / HHsearch | pairwise comparison of pro | Protein | server download | S?ding J | |
IDF | Inverse Document Frequency | Both | download | ||
Infernal | pro | RNA | download | Eddy S | |
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, Sch?ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, NCBI | 1997 |
SAM | local and global search with pro | Both | SAM | Karplus K, Krogh A | |
SSEARCH | Smith-Waterman search, slower but more sensitive than FASTA | Both | EBI DDBJ | ||
*Sequence Type: Protein or nucleotide |
Name | Description | Sequence Type* | Alignment Type** | Link | Author | Year |
---|---|---|---|---|---|---|
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. | 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 |
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 |
LALIGN | Multiple, non-overlapping, local similarity (same algorithm as SIM) | Both | Local non-overlapping | server FASTA server | W. Pearson | 1991 (algorithm) |
mAlign | modelling alignment; models the information content of the sequences | Nucleotide | Both | [1] [2] | D. Powell, L. Allison and T. I. Dix | 2004 |
matcher | Memory-optimized Needleman-Wunsch dynamic programming (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 | 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. G?rdea et al. | 2009 |
PatternHunter | Seeded pattern-matching | Nucleotide | Local | download | B. Ma et al. | 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 |
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 |
SLIM Search | Ultra-fast blocked alignment | Both | Both | site | S. Inglis, J. Cleary, S. Irvine, L. Trigg, L. Bloksberg et al. | 2004 |
SSEARCH | Local (Smith-Waterman) alignment with statistics | Protein | Local | EBI FASTA server | W. Pearson | 1981 (Algorithm) |
Sequences Studio | Java applet demonstrating various algorithms from [1] | Generic sequence | Local and global | co | A.Meskauskas | 1997 (reference book) |
SWIFT suit | Fast Local Alignment Searching | DNA | Local | site | K. Rasmussen, W. Gerlach | 2005,2008 |
stretcher | Memory-optimized but slow 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 |
water | Smith-Waterman dynamic programming | Both | Local | 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 | 2003-2007 |
*Sequence Type: Protein or nucleotide. **Alignment Type: Local or global |
Name | Description | Sequence Type* | Alignment Type** | Link | Author | Year |
---|---|---|---|---|---|---|
ABA | A-Bruijn alignment | Protein | Global | download | B.Raphaelet al. | 2004 |
ALE | manual alignment ; some software assistance | Nucleotides | Local | download | J. Blandy and K. Fogel | 1994 (latest version 2007) |
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 2009) |
CHAOS/DIALIGN | Iterative alignment | Both | Local (preferred) | server | M. Brudno and B. Morgenstern | 2003 |
ClustalW | Progressive alignment | Both | Local or Global | download EBI DDBJ PBIL EMBNet GenomeNet | Thompson et al. | 1994 |
CodonCode Aligner | Multi alignment; ClustalW & Phrap support | Nucleotides | Local or Global | download | P. Richterich et al. | 2003 (latest version 2009) |
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) |
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 | serverEBI MPItoolkit | T. Lassmann | 2005 |
MSA | Dynamic programming | Both | Local or Global | download | D.J. Lipman et al. | 1989 (modified 1995) |
PRRN/PRRP | Iterative alignment (especially refinement) | Protein | Local or Global | PRRP PRRN | Y. Totoki (based on O. Gotoh) | 1991 and later |
POA | Partial order/hidden Markov model | Protein | Local or Global | download | C. Lee | 2002 |
SAM | Hidden Markov model | Protein | Local or Global | server | A. Krogh et al. | 1994 (most recent version 2002) |
MARNA | Multiple Alignment of RNAs | RNA | Local | server download | S. Siebert et al. | 2005 |
MAFFT | Progressive/iterative alignment | Both | Local or Global | GenomeNet MAFFT | K. Katoh et al. | 2005 |
MAVID | Progressive alignment | Both | Global | server | N. Bray and L. Pachter | 2004 |
MULTALIN | Dynamic programming/clustering | Both | Local or Global | server | 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 |
Pecan | Probabilistic/consistency | DNA | Global | download | B. Paten et al. | 2008 |
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 |
PSAlign | Alignment preserving non-heuristic | Both | Local or Global | download | S.H. Sze, Y. Lu, Q. Yang. | 2006 |
SAGA | Sequence alignment by genetic algorithm | Protein | Local or Global | download | C. Notredame et al. | 1996 (new version 1998) |
StatAlign | Bayesian co-estimation of alignment and phylogeny (MCMC) | Both | Global | download | A. Novak et al. | 2008 |
T-Coffee | More sensitive progressive alignment | Both | Local or Global | server download | C. Notredame et al. | 2000 (newest version 2008) |
Tuiuiu | Seeded filtration | Nucleotides | Local | server | P. Peterlongo et al. | 2009 |
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) |
UGENE | Supports multiple alignment with MUSCLE plugin, local sequences alignment with Smith-Waterman algorithm. | Both | Local or Global | download | UGENE team | 2009 |
*Sequence Type: Protein or nucleotide. **Alignment Type: Local or global |
Name | Description | Sequence Type* | Link |
---|---|---|---|
SLAM | Gene finding, alignment, annotation (human-mouse homology identification) | Nucleotide | server |
Mauve | Multiple alignment of rearranged genomes | 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 |
Sequerome | Profiling sequence alignment da | Nucleotide/peptide | server |
AVID | Pairwise global alignment with whole genomes | Nucleotide | server |
SIBsim4 / Sim4 | A program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns | Nucleotide | download |
Shuffle-LAGAN | Pairwise glocal alignment of completed genome regions | Nucleotide | server |
ACT (Artemis Comparison Tool) | Synteny and comparative genomics | Nucleotide | server |
*Sequence Type: Protein or nucleotide |
Name | Description | Sequence Type* | Link |
---|---|---|---|
MEME/MAST | Motif discovery and search | Both | 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 (on |
HMMTOP | Prediction of transmembrane helices and topology of proteins | Protein | homepage & download |
TEIRESIAS | Motif extraction and database search | Both | server |
PRATT | Pattern generation for use with ScanProsite | Protein | server |
ScanProsite | Motif database search tool | Protein | server |
PHI-Blast | Motif search and alignment tool | Both | Pasteur |
I-sites | Local structure motif library | Protein | server |
*Sequence Type: Protein or nucleotide |
Name | Link | Authors |
---|---|---|
BAliBASE | download | Thompson, Plewniak, Poch |
HOMSTRAD | download | Stebbings, 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 |
Please see the List of alignment visualization software.
Name | Description | Multi-threaded | License | Link |
---|---|---|---|---|
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) | GPL | link |
CASHX | Quantify and manage large quantities of short-read sequence da | No | Free for academic and non-commercial use. | link |
MAQ | Ungapped alignment that takes into account quality scores for each base. | GPL | link | |
Novoalign | Gapped alignment of single end and paired end Illumina GA I & II reads and reads from the new Helicos Heliscope Genome Analyzer. High sensitivity and specificity, using base qualities at all steps in the alignment. | Multi-threading available with paid license. | Single threaded version free for academic and non-commercial use. | Novocraft |
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 |
ELAND | Implemented by Illumina. Includes ungapped alignment with a finite read length. | |||
SeqMap | Up to 5 mixed substitutions and insertions/deletions. Various tuning options and input/output formats. | Free for academic and non-commercial use. | link | |
SSAHA and SSAHA2 | Fast for a small number of variants. | Free for academic and non-commercial use. | link | |
SLIM Search | Extremely fast, tolerant to high indel and substitution counts. Includes full read alignment. | Yes | Commercial/High-use customers can join beta programme (Q2 '09) | link |
SOAP | Robust with a small (1-3) number of gaps and mismatches. Speed improvement over BLAT, uses a 12 letter hash table.Now SOAP2 is much faster than the first version. | YES(MULTITHREAD) | GPL; SOAP2 source is currently unavailable | link |
BLAT | Made by Jim Kent. Can handle on | Yes (client/server). | Free for academic and non-commercial use. | link |
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 | ||
ZOOM | Reads can vary between 25bp and 64bp in length. Fast but not accurate for >2 mismatches. Ignores insertions and deletions. | Commercial | link | |
RMAP | Read lengths can range from 20bp to at most 64bp. Uses the "exclusion principle" to allow for mismatches and look-up reads in an index. | link | ||
SHRiMP | Indexes the reads instead of the reference genome. Uses masks to generate possible keys. Can map ABI SOLiD color space reads. | BSD derivative | 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 | |
Bowtie | Uses a Burrows-Wheeler 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 (POSIX) | Artistic License | link |
QPalma | Uses known alignments to align targeted spliced reads. Useful for transcriptome resequencing and gene exploration. | Yes (client/server) | GPLv2 | link |
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 | link | |
MOSAIK | Fast and incorporates assembly. Aligns reads using a hashing scheme. Must split the reads many times to be robust against increasing number of mismatches. | Yes | link | |
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 | ||
MOM | MOM or maximum oligonucleotide mapping is a query matching tool that captures a maximal length match within the short read. | Yes | [3]- |
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