MAFFT
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.
It is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
Important note: This tool can align up to 500 sequences or a maximum file size of 1 MB.