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
|
| FASTA
|
k-tuple local search |
Both |
EBI GenomeNet PIR (protein only)
|
| BLAST
|
k-tuple local search (Basic Local Alignment Search Tool) |
Both |
NCBI EBI GenomeNet PIR (protein only)
|
| SSEARCH
|
Smith-Waterman search (more sensitive than FASTA) |
Both |
server
|
| HMMer
|
Hidden Markov profile search |
Protein/DNA |
download (S. Eddy)
|
| SAM
|
Hidden Markov profile search |
Protein/DNA |
SAM (K. Karplus, A. Krogh)
|
| Combinatorial Extension
|
Structural alignment search |
Protein |
server
|
| IDF
|
Inverse Document Frequency |
Both |
Download
|
| *Sequence Type: Protein or nucleotide
|
Pairwise alignment
| Name
|
Description |
Sequence Type* |
Alignment Type** |
Link |
Author |
Year
|
| 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
|
| JAligner
|
Open source Java implementation of Smith-Waterman |
Both |
Local |
JWS |
A. Moustafa |
2005
|
| LALIGN
|
Local similarity (same algorithm as SIM) |
Both |
Local (default) or global |
server |
B. Pearson |
1991 (algorithm)
|
| matcher
|
Memory-optimized needleman but slow dynamic programming (based on LALIGN) |
Both |
Local |
server |
I. Longden (modified from B. 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
|
| 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 |
2003-2006
|
| BioPerl dpAlign
|
dynamic programming |
Both |
Both + Ends-free |
site |
Y. M. Chan |
2003
|
| *Sequence Type: Protein or nucleotide. **Alignment Type: Local or global
|
Multiple sequence alignment
| Name
|
Description |
Sequence Type* |
Alignment Type** |
Link |
Author |
Year
|
| ABA
|
A-Bruijn alignment |
Protein |
Global |
download |
B.Raphaelet al. |
2004
|
| ClustalW
|
Progressive alignment |
Both |
Local or Global |
EBI PBIL EMBNet GenomeNet |
Thompson et al. |
1994
|
| AMAP
|
Sequence annealing |
Both |
Global |
server |
A. Schwartz and L. Pachter |
2006
|
| CodonCode Aligner
|
Multi alignment; ClustalW & Phrap support |
Nucleotides |
Local or Global |
download |
P. Richterich et al. |
2003 (latest version 2007)
|
| BAli-Phy
|
Tree+Multi alignment ; Probabilistic/Bayesian ; Joint Estimation |
Both |
Global |
WWW+download |
BD Redelings and MA Suchard |
2005 (latest version 2007)
|
| 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
|
| CHAOS/DIALIGN
|
Iterative alignment |
Both |
Local (preferred) |
server |
M. Brudno and B. Morgenstern |
2003
|
| Kalign
|
Progressive alignment |
Both |
Global |
serverEBI MPItoolkit |
T. Lassmann |
2005
|
| 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
|
| MSA
|
Dynamic programming |
Both |
Local or Global |
download |
D.J. Lipman et al. |
1989 (modified 1995)
|
| SAM
|
Hidden Markov model |
Protein |
Local or Global |
server |
A. Krogh et al. |
1994 (most recent version 2002)
|
| ProbCons
|
Probabilistic/consistency |
Protein |
Local or Global |
server |
C. Do et al. |
2005
|
| MULTALIN
|
Dynamic programming/clustering |
Both |
Local or Global |
server |
F. Corpet |
1988
|
| MAVID
|
Progressive alignment |
Both |
Global |
server |
N. Bray and L. Pachter |
2004
|
| 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
|
| MAFFT
|
Progressive/iterative alignment |
Both |
Local or Global |
GenomeNet MAFFT |
K. Katoh 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
|
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
|
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
|
Benchmarking
| Name
|
Link
|
Authors
|
| BAliBASE
|
download
|
Thompson, Plewniak, Poch
|
| Prefab
|
download
|
Edgar
|
External links
