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| [[Geneious]]
| Progressive-Iterative alignment; ClustalW plugin || Both || Local or global || A.J. Drummond ''et al.'' || 2005 (latest version 2017) ||
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| GUIDANCE
| Quality control and filtering of multiple sequence alignments || Both || Local or global || O. Penn ''et al.'' || 20010 (latest version 2015) ||
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| Kalign
|