ClustalW is a general-purpose multiple sequence alignment program for nucleotide sequences or proteins. The alignments can be either global (whole sequences) or local (restricted to subsequences). ClustalW calculates the best match for the selected sequences, and lines them up so that the identities, similarities, and differences can be seen. For details see Section 9.2 at the end of this chapter. We're using Version 1.82 of ClustalW.
An example of a ClustalW command-line entry:
clustalw -infile=file.txt -align
where file.txt contains the FASTA-formatted sequences.