A user manual will eventually arrive here (before official release of a non-beta version of Opal).

Java >= 1.4 is required.

Here's a simple list of commands:
   java -jar Opal.x.x.x.jar --in infile.fasta --out outfile
or
   java -jar Opal.x.x.x.jar < infile.fasta > outfile

Note: input files must be in fasta format

Optional arguments:
--in2 filename (with this option, an alignment of two alignments is performed. The two files specified in "--in" and "--in2" must both contain alignments)
--align_method [exact|profile] (default = exact; profile is much faster for large inputs)
--out_format [fasta|clustalw] (default = fasta)
--polish_reps n (default: using exact algorithm, 30; using profile heuristic, 100)
--gamma n (Gap open penalty. Default = 60)
--lambda n (Gap extension penalty. Default = 38)
--gamma_term n (Open penalty for terminal gaps. Default = 15)
--lambda_term n (Extension penalty for terminal gaps. Default = 36)

Details of the algorthms used in Opal are available in this paper.

The paper was presented at ISMB 2007. I'm making available an extended version of the Powerpoint slides used in that presentation. Feel free to use these slides in any way you see fit, with proper reference to the source.