| 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)
|
| GGSEARCH / GLSEARCH
| Global:Global (GG), Global:Local (GL) alignment with statistics | Protein | FASTA server
|
| SSEARCH
| Smith-Waterman search (more sensitive than FASTA) | Both | EBI 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
|
| 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
|
| 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 | 2003-2006
|
| BioPerl dpAlign
| dynamic programming | Both | Both + Ends-free | site | Y. M. Chan | 2003
|
| *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
|
| 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
|
| 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
|
| 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
|
