Pairwise Alignment
| Name | Description | Sequence Type* | Alignment Type** | Link | Author | Year |
|---|---|---|---|---|---|---|
| ACANA | fast heuristic anchor based pairwise alignment | Both | Both | download | Huang, Umbach, Li | 2005 |
| AlignMe | Alignments for low identity membrane protein sequences based on various similarity criteria | Protein | Both | download,server | K. Khafizov, R. Staritzbichler, M. Stamm, L.R. Forrest | 2010 |
| Bioconductor Biostrings::pairwiseAlignment | Dynamic programming | Both | Both + Ends-free | site | P. Aboyoun | 2008 |
| BioPerl dpAlign | Dynamic programming | Both | Both + Ends-free | site | Y. M. Chan | 2003 |
| BLASTZ,LASTZ | Seeded pattern-matching | Nucleotide | Local | download,download | Schwartz et al. | 2004,2009 |
| 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 |
| FEAST | Posterior based local extension with descriptive evolution model | Nucleotide | Local | site | A. K. Hudek and D. G. Brown | 2010 |
| G-PAS | GPU-based dynamic programming with backtracking | Both | Local, SemiGlobal, Global | site+download | W. Frohmberg, M. Kierzynka et al. | 2011 |
| GapMis | GapMis is a tool for pairwise sequence alignment with a single gap | Both | SemiGlobal | site | K. Frousios, T. Flouri, C. S. Iliopoulos, K. Park, S. P. Pissis, G. Tischler | 2012 |
| 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 |
| K*Sync | Protein sequence to structure alignment that includes secondary structure, structural conservation, structure-derived sequence profiles, and consensus alignment scores | Protein | Both | Robetta server | D. Chivian & D. Baker | 2003 |
| LALIGN | Multiple, non-overlapping, local similarity (same algorithm as SIM) | Both | Local non-overlapping | server FASTA server | W. Pearson | 1991 (algorithm) |
| mAlign | modelling alignment; models the information content of the sequences | Nucleotide | Both | doc code | D. Powell, L. Allison and T. I. Dix | 2004 |
| matcher | Memory-optimized Needleman-Wunsch dynamic programming (based on LALIGN) | Both | Local | Pasteur | 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 | SemiGlobal | EBIPasteur | A. Bleasby | 1999 |
| Ngila | logarithmic and affine gap costs and explicit models of indel evolution | Both | Global | download | R. Cartwright | 2007 |
| Path | Smith-Waterman on protein back-translation graph (detects frameshifts at protein level) | Protein | Local | server download | M. Gîrdea et al. | 2009 |
| 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 |
| SABERTOOTH | Alignment using predicted Connectivity Profiles | Protein | Global | download on request | F. Teichert, J. Minning, U. Bastolla, and M. Porto | 2009 |
| Satsuma | Parallel whole-genome synteny alignments | DNA | Local | download | M.G. Grabherr et al. | 2010 |
| 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 |
| SPA: Super pairwise alignment | Fast pairwise global alignment | Nucleotide | Global | available upon request | Shen, Yang, Yao, Hwang | 2002 |
| SSEARCH | Local (Smith-Waterman) alignment with statistics | Protein | Local | EBI FASTA server | W. Pearson | 1981 (Algorithm) |
| Sequences Studio | Java applet demonstrating various algorithms from | Generic sequence | Local and global | code applet | A.Meskauskas | 1997 (reference book) |
| SWIFT suit | Fast Local Alignment Searching | DNA | Local | site | K. Rasmussen, W. Gerlach | 2005,2008 |
| stretcher | Memory-optimized dynamic programming | Both | Global | Pasteur | I. Longden (modified from G. Myers and W. Miller) | 1999 |
| tranalign | Aligns nucleic acid sequences given a protein alignment | Nucleotide | NA | Pasteur | G. Williams (modified from B. Pearson) | 2002 |
| UGENE | Opensource Smith-Waterman for SSE/CUDA, Suffix array based repeats finder & dotplot | Both | Both | UGENE site | UniPro | 2010 |
| water | Smith-Waterman dynamic programming | Both | Local | EBIPasteur | A. Bleasby | 1999 |
| wordmatch | k-tuple pairwise match | Both | NA | Pasteur | I. Longden | 1998 |
| YASS | Seeded pattern-matching | Nucleotide | Local | server download | L. Noe and G. Kucherov | 2003–2007 |
Read more about this topic: List Of Sequence Alignment Software