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)
|
CodonCode Aligner
| Multi alignment; ClustalW & Phrap support | Nucleotides | Local or Global | download | P. Richterich et al. | 2003 (latest version 2007)
|
ClustalW
| Progressive alignment | Both | Local or Global | EBI PBIL EMBNet GenomeNet | Thompson et al. | 1994
|
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
|