Sequence similarity searches can be done in multiple ways on multiple platforms. BLAST (Basic Local Alignment Search Tool) aligns a sequence to a database of other sequences or can align two sequences to each other. BLAST can be done with nucleotide sequences or with amino acid protein sequences. There are a number of special BLAST variations that allow searching among more dissimilar sequences. Multiple sequence alignment (done by CLUSTAL, COBALT, MUSCLE, ProbCons and others) consists of aligning several sequences to each other.
Specialized BLAST tools are available for many purposes; choosing the right BLAST tool and utilizing it properly can help you: