ClustalW [1, 2] is one of the most commonly used tools for Multiple Sequence Alignment because it is fast and generally accurate enough for a general set of questions. Other tools such as MUSCLE, MAFFT, PROBCONS, T-Coffee provide more accuracy, sometimes with comparable speed. The software is available here as well as the graphical version, ClustalX .
The ClustalW multiple alignment format is a human and computer readable format that represents the alignment in ASCII text. Several other output options are available from the command line and interactive menu driven application.
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