Sequence Alignment Software
See also:
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 |
| 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 |
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 |
EBIserver |
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 |
EBI 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 |
EBIPasteur 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 |
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) |
| 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 (latest version 2008) |
| 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 |
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 |
| 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 |
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.
External links
- Pollard et al. (2004) (PubMed Central free fulltext): The authors discuss LAGAN, CHAOS, and Dialign as the most effective tools tested for certain uses.
This article is licensed under the GNU Free Documentation License. It uses material from Wikipedia Encyclopedia article "Sequence Alignment Software"
|
|
