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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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