Sequence alignment software
Pairwise sequence alignment and multiple sequence alignment software list
See structural alignment software for Structural alignment of proteins.
Contents
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) |
| 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 | |||
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 |
| 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 | ||||||
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) |
| 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 | ||||||
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
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.