Multiple Sequence Alignment
| Name | Description | Sequence Type* | Alignment Type** | Link | Author | Year | License |
|---|---|---|---|---|---|---|---|
| ABA | A-Bruijn alignment | Protein | Global | download | B.Raphaelet al. | 2004 | Proprietary, without charge for educational, research and non profit. |
| ALE | manual alignment ; some software assistance | Nucleotides | Local | download | J. Blandy and K. Fogel | 1994 (latest version 2007) | GPL2 |
| AMAP | Sequence annealing | Both | Global | server | A. Schwartz and L. Pachter | 2006 | |
| anon. | fast, optimal alignment of three sequences using linear gap costs | Nucleotides | Global | paper software | D. Powell, L. Allison and T. I. Dix | 2000 | |
| BAli-Phy | Tree+Multi alignment ; Probabilistic/Bayesian ; Joint Estimation | Both | Global | WWW+download | BD Redelings and MA Suchard | 2005 (latest version 2010) | |
| Base-By-Base | Java-based multiple sequence alignment editor with integrated analysis tools | Both | Local or Global | download | R. Brodie et al. | 2004 | Free, requires registration. |
| 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 | GNU Lesser GPL |
| CodonCode Aligner | Multi alignment; ClustalW & Phrap support | Nucleotides | Local or Global | download | P. Richterich et al. | 2003 (latest version 2009) | |
| DIALIGN-TX and DIALIGN-T | Segment-based method | Both | Local (preferred) or Global | download and server | A.R.Subramanian | 2005 (latest version 2008) | |
| DNA Alignment | Segment-based method for intraspecific alignments | Both | Local (preferred) or Global | server | A.Roehl | 2005 (latest version 2008) | |
| DNA Baser Sequence Assembler | Multi alignment; Automatic batch alignment | Nucleotides | Local or Global | www.DnaBaser.com | Heracle BioSoft | 2012 | |
| FSA | Sequence annealing | Both | Global | download and server | R. K. Bradley et al. | 2008 | |
| Geneious | Progressive/Iterative alignment; ClustalW plugin | Both | Local or Global | download | A.J. Drummond et al. | 2005 (latest version 2009) | |
| Kalign | Progressive alignment | Both | Global | serverEBI MPItoolkit | T. Lassmann | 2005 | |
| MAFFT | Progressive/iterative alignment | Both | Local or Global | GenomeNet MAFFT | K. Katoh et al. | 2005 | |
| MARNA | Multiple Alignment of RNAs | RNA | Local | server download | S. Siebert et al. | 2005 | |
| MAVID | Progressive alignment | Both | Global | server | N. Bray and L. Pachter | 2004 | |
| MSA | Dynamic programming | Both | Local or Global | download | D.J. Lipman et al. | 1989 (modified 1995) | |
| MSAProbs | Dynamic programming | Protein | Global | download | Y. Liu, B. Schmidt, D. Maskell | 2010 | |
| 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 | |
| Opal | Progressive/iterative alignment | Both | Local or Global | download | T. Wheeler and J. Kececioglu | 2007 | |
| Pecan | Probabilistic/consistency | DNA | Global | download | B. Paten et al. | 2008 | |
| Phylo | A human computing framework for comparative genomics to solve multiple alignment | Nucleotides | Local or Global | site | McGill Bioinformatics | 2010 | |
| Praline | Progressive/iterative/consistency/homology-extended alignment with pre-profiling and secondary structure prediction | Protein | Global | server | J. Heringa | 1999 (latest version 2009) | |
| POA | Partial order/hidden Markov model | Protein | Local or Global | download | C. Lee | 2002 | |
| Probalign | Probabilistic/consistency with partition function probabilities | Protein | Global | server | Roshan and Livesay | 2006 | |
| ProbCons | Probabilistic/consistency | Protein | Local or Global | server | C. Do et al. | 2005 | |
| PROMALS3D | Progressive alignment/hidden Markov model/Secondary structure/3D structure | Protein | Global | server | J. Pei et al. | 2008 | |
| PRRN/PRRP | Iterative alignment (especially refinement) | Protein | Local or Global | PRRP PRRN | Y. Totoki (based on O. Gotoh) | 1991 and later | |
| PSAlign | Alignment preserving non-heuristic | Both | Local or Global | download | S.H. Sze, Y. Lu, Q. Yang. | 2006 | |
| 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) | |
| SAGA | Sequence alignment by genetic algorithm | Protein | Local or Global | download | C. Notredame et al. | 1996 (new version 1998) | |
| SAM | Hidden Markov model | Protein | Local or Global | server | A. Krogh et al. | 1994 (most recent version 2002) | |
| Se-Al | Manual alignment | Both | Local | download | A. Rambaut | 2002 | |
| StatAlign | Bayesian co-estimation of alignment and phylogeny (MCMC) | Both | Global | download | A. Novak et al. | 2008 | |
| Stemloc | Multiple alignment and secondary structure prediction | RNA | Local or Global | download | I. Holmes | 2005 | GPLv3 (parte de DART) |
| T-Coffee | More sensitive progressive alignment | Both | Local or Global | server download | C. Notredame et al. | 2000 (newest version 2008) | GPL2 |
| UGENE | Supports multiple alignment with MUSCLE, KAlign, Clustal and MAFFT plugins | Both | Local or Global | download | UGENE team | 2010 (newest version 2012) | GPL2 |
Read more about this topic: List Of Sequence Alignment Software
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