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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.
[edit] Database search only
| Name |
Description |
Sequence Type* |
Link |
| BLAST |
k-tuple local search (Basic Local Alignment Search Tool) |
Both |
NCBI EBI DDBJ DDBJ (psi-blast) GenomeNet PIR (protein only) |
| Combinatorial Extension |
Structural alignment search |
Protein |
server |
| FASTA |
k-tuple local search |
Both |
EBI DDBJ GenomeNet PIR (protein only) |
| GGSEARCH / GLSEARCH |
Global:Global (GG), Global:Local (GL) alignment with statistics |
Protein |
FASTA server |
| HMMER |
Hidden Markov profile search |
Protein/DNA |
download (S. Eddy) DDBJ (HMMPFAM) |
| IDF |
Inverse Document Frequency |
Both |
Download |
| Infernal |
profile SCFG search |
RNA |
download (S. Eddy) |
| SAM |
Hidden Markov profile search |
Protein/DNA |
SAM (K. Karplus, A. Krogh) |
| SSEARCH |
Smith-Waterman search (more sensitive than FASTA) |
Both |
EBI DDBJ server |
| *Sequence Type: Protein or nucleotide |
[edit] Pairwise alignment
| Name |
Description |
Sequence Type* |
Alignment Type** |
Link |
Author |
Year |
| BioPerl dpAlign |
dynamic programming |
Both |
Both + Ends-free |
site |
Y. M. Chan |
2003 |
| BLASTZ |
Seeded pattern-matching |
Nucleotide |
Local |
download |
Schwartz et al. |
2003 |
| 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) |
| matcher |
Memory-optimized needleman but slow dynamic programming (based on LALIGN) |
Both |
Local |
server |
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 |
Global |
server |
A. Bleasby |
1999 |
| Ngila |
logarithmic and affine gap costs and explicit models of indel evolution |
Both |
Global |
download |
R. Cartwright |
2007 |
| 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 |
| 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 |
L. Bloksberg |
2004 |
| SSEARCH |
Local (Smith-Waterman) alignment with statistics |
Protein |
Local |
FASTA server |
W. Pearson |
1981 (Algorithm) |
| stretcher |
Memory-optimized but slow dynamic programming |
Both |
Global |
server |
I. Longden (modified from G. Myers and W. Miller) |
1999 |
| tranalign |
Aligns nucleic acid sequences given a protein alignment |
Nucleotide |
NA |
server |
G. Williams (modified from B. Pearson) |
2002 |
| water |
Smith-Waterman dynamic programming |
Both |
Local |
server |
A. Bleasby |
1999 |
| wordmatch |
k-tuple pairwise match |
Both |
NA |
server |
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 |
Ŷ
[edit] Multiple sequence alignment
| 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 |
| BAli-Phy |
Tree+Multi alignment ; Probabilistic/Bayesian ; Joint Estimation |
Both |
Global |
WWW+download |
BD Redelings and MA Suchard |
2005 (latest version 2007) |
| 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 2007) |
| DIALIGN-TX and DIALIGN-T |
Segment-based method |
Both |
Local (preferred) or Global |
download and server |
A.R.Subramanian |
2005 (latest version 2008) |
| DNA Baser |
Multi alignment |
Both |
Local or Global + Post processing |
DNA Baser (commercial) |
M. Gabriel |
released 2005 |
| Ed'Nimbus |
Seeded filtration |
Nucleotides |
Local |
server |
P. Peterlongo et al. |
2006 |
| Geneious |
Progressive/Iterative alignment; ClustalW plugin |
Both |
Local or Global |
download |
A.J. Drummond et al. |
2005 / 2006 |
| 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) |
| 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 |
| 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) |
| T-Coffee |
More sensitive progressive alignment |
Both |
Local or Global |
server |
C. Notredame et al. |
2000 |
| 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) |
| *Sequence Type: Protein or nucleotide. **Alignment Type: Local or global |
[edit] Genomics analysis
| 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 |
| Sequerome |
Profiling sequence alignment data with major servers/services |
Nucleotide/peptide |
[1] |
| 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 |
[edit] Motif finding
| 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 (one of many implementations) |
| 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 |
server |
| I-sites |
Local structure motif library |
Protein |
server |
| *Sequence Type: Protein or nucleotide |
[edit] Benchmarking
| 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 |
[edit] Viewers
Jalview is a Java multiple sequence alignment viewer, which is used to integrate the results of a secondary structure prediction via the JPred web server with a multiple sequence alignment given as input or derived during the run of the algorithm.
[edit] External links
