If you use Opal from within Mesquite, please cite the paper that describes Opal:
Wheeler, T. J., & Kececioglu, J. D. 2007. Multiple alignments by aligning alignments. Bioinformatics, 23, i559-i568.
For more details about Opal's options, see Opal's web site or by reading the README file.
For more details about using Opal within Mesquite, see the documentation for Opalescent.