Running ClustalW by command line

1. Run the command "clustalw".
2. Select option 1 "Sequence Input From Disc" and introduce the name of the file with FASTA formatted sequences.
3. Select option 2 "Multiple alignments".
4. Select option 9 "Output format options". Now select option 3 "Toggle GCG/MSF format output" to save the output in "MSF" format.
5. Hit "Return", to go back to the previous menu.
6. Select option 1 "Do complete multiple alignment now (Slow/Accurate)" and accept or assign a name to the files that will generate ClustalW.
7.  ClustalW will make all against all pairwise comparisons to generate a guide tree, and then it will start making the alignment, and saving it into a file.
8. Three files will be generated:

• one with the extension "dnd", that contains the guide tree
• one with the extension "aln", which contains the alignment in ClustalW format.
• one with the extension "msf", which contains the alignment in MSF format.