Example 1: to align a set of fasta format sequences:
    command: pcma 1aboA_ref2.fa -ave_grp_id=50 -outfile=1aboA_ref2.pcma50.aln

Example 2: to align a list of alignments, alnlist contains the names of
	   the input alignments.  The first line of alnlist begins with
	   a '@' character.
    command: pcma alnlist
