There are numerous methods available for generating multiple sequence alignments (MSAs). Classic methods such as ClustalW (Thompson, et al., 1994) can give reasonably accurate results for similar sequences, but fail to produce accurate alignments for divergent sequences (Thompson, et al., 1999). However, a perfect MSA method does not exist and that individual methods have their specific strengths and weaknesses. The most widely used and state of the art sequence alignment methods are listed here.
M-Coffee |
http://www.tcoffee.org/ |
(Wallace, et al., 2006) |
MAFFT |
http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ |
(Katoh, et al., 2005; Katoh, et al., 2002) |
PROBCONS |
http://probcons.stanford.edu/ |
(Do, et al., 2005) |
PROMALS |
http://prodata.swmed.edu/promals/ |
(Pei, et al., 2007) |
ClustalW2 |
http://www.ebi.ac.uk/Tools/clustalw2/index.html |
(Larkin, et al., 2007) |
MUSCLE |
http://www.ebi.ac.uk/Tools/muscle/index.html |
(Edgar, 2004) |
Ready-made sequence alignments for protein families are available in the Pfam database (Finn, et al., 2008) at http://pfam.sanger.ac.uk/.
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