for filename in sys argv sequences read_FASTA_sequences filename each

for filename in sys.argv[1:]:
	sequences = read_FASTA_sequences(filename)
	#each sequence is a single cluster
	#calc first table
	A = np.zeros((len(sequences), len(sequences)))
	for i in xrange(len(sequences):
		for j in xrange(len(sequences)):
			if i == j: continue
			os.system("./pairwise " + sequences[i] + " " + sequences[j])