Clustal Omega (Clustal-O) is a program to perform a multiple sequence alignment (MSA).
You can read the manual of clustal-o in HERE
USAGE
The input information of the proteins for the alignment must be in FASTA format and you may choose one of these 3 options. The output file of the alignment can be chosen below. For the second option, when entering UniProt Ids separate them with white spaces, other separators will not be recognised.