| Table 5.1. Examples of programs for multiple sequence alignment |
| Name |
|
Uses |
|
Reference |
|
|
| Global alignments including progressive |
| CLUSTALW |
standard progressive alignment |
Thompson et al. (1994a, 1997) |
| CLUSTALX (graphical interface) |
most useful for similar sequences |
Higgins et al. (1996) |
| MAFFT: rapid multiple sequence alignment based on Fourier transform (progressive and iterative programs) |
fast, accurate msa alignments with novel scoring systems |
Katoh et al. (2002) |
| MAVID for progressive msa of genome sequences |
progressive alignment method for large numbers of DNA sequences with viewer |
Bray and Pachter (2003) |
| MSA |
optimal alignment using dynamic programming—limited to few/short sequences |
Lipman et al. (1989); Gupta et al. (1995) |
| MULTIPIPMAKER |
produces percent identity plot of multiple DNA sequences |
Schwartz et al. (2003) |
| POA |
fast, accurate alignment of large numbers of sequences (ESTs) by partial-order graphs |
Lee et al. (2002) |
| PRALINE |
versatile tool kit for producing msa's by different strategies |
Heringa (1999); Simossis and Heringa (2003) |
| T-COFFEE |
uses CLUSTALW method but with pair-wise alignments to increase accuracy; flexible |
Poirot et al. (2003) |
| Iterative and other methods |
| DIALIGN |
segment alignment; very accurate msa method for DNA and protein sequences; aligns based on matching segments without gap penalties |
Morgenstern et al. (1998) |
| PRRP |
progressive global alignment method repeatedly improves msa; produced by progressive alignment using command line options |
Gotoh (1996) |
| SAGA |
genetic algorithm; user intense method based on biologically relevant method |
Notredame and Higgins (1996) |
| Local alignments of proteins |
| Aligned Segment Statistical Evaluation Tool (Asset) |
sophisticated pattern-finding and statistical analysis method—command line |
Neuwald and Green (1994) |
| BLOCKS Web site |
finds blocks (ungapped domains) by pattern search or Gibbs sampling |
Henikoff and Henikoff (1991, 1992) |
| eMOTIF Web server |
useful analysis of protein families to find most significant patterns in families |
Nevill-Manning et al. (1998) |
| GIBBS, the Gibbs sampler statistical method |
finds patterns in unaligned sequences by statistical method—command line |
Lawrence et al. (1993); Liu et al. (1995); Neuwald et al. (1995) |
| HMMER |
hidden Markov model software tools for producing a profile hidden Markov model to represent an msa |
Eddy (1998) |
| MACAW, a workbench for multiple alignment construction and analysis |
aligner/editor for locating and adjusting local alignment blocks on PC |
Schuler et al. (1991) |
| MEME Web site, expectation maximization method |
locates localized sequence blocks "motifs" by statistical method |
Bailey and Elkan (1995); Grundy et al. (1996, 1997); Bailey and Gribskov (1998) |
| Profile analysis at UCSD |
produces a sequence profile from an msa |
Gribskov and Veretnik (1996) |
| SAM hidden Markov model Web site |
produces an HMM for an msa |
Krogh et al. (1994); Hughey and Krogh (1996) |
|
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