A software package that allows one to carry out multiple alignment of protein and nucleic acid sequences of almost unlimited length and number of sequences is developed on C-DAC parallel computer—a transputer-based machine. The farming approach is used for data parallelization. The speed gains are almost linear when the number of transputers is increased from 4 to 64. The software is used to carry out multiple alignment of 100 sequences each of α-chain and β-chain of hemoglobin and 83 cytochrome c sequences. The signature sequence of cytochrome c was found to be PGTKMXF. The single parameter, multiple alignment score, S, has been used to categorize proteins in different subfamilies and groups.