Java ≥ 5 (aka v1.5) is required.

Opal is software for aligning multiple biological sequences. It can align 
both protein and DNA sequences, and expects inputs to be in fasta format.

In benchmark tests, Opal aligns sequences with good accuracy. On DNA, 
accuracy is similar to that of MAFTT and Muscle; on protein, accuracy is 
similar to MAFFT, and better than Muscle. 

Details of the algorithms used in Opal are available in the original ISMB 
paper, which should be cited in the event Opal is used:
   Wheeler, T.J. and Kececioglu, J.D.
   Multiple alignment by aligning alignments,
   Proceedings of the 15th ISCB Conference on Intelligent Systems  
   for Molecular Biology (ISMB), Bioinformatics 23, i559-i568, 2007.
   
Significant acceleration with negligible loss in accuracy was achieved
after publication of that paper, through heuristic guide-tree construction 
(similar to the approach used in MAFFT and Muscle).

Additional accuracy on protein sequence alignment is achieved by using a 
modified scoring scheme that incorporates protein secondary structure, as 
predicted by psipred. Details of this approach are available in the following 
paper, which should be cited if secondary-structure-based alignment is 
performed: 
   Kim, E., Wheeler, T.J., and Kececioglu, J.D.  Learning models for aligning
   protein sequence with predicted secondary structure, Proceedings of the 
   13th Conference on Research in Computational Molecular Biology (RECOMB), 
   Springer-Verlag Lecture Notes in Bioinformatics 5541: 586-605, 2009.

Quick-start
-----------

(1) After downloading opal.tgz, unpack with the command
       tar -xzf Opal.tgz
This will create a folder opal_x.y.z, containing four files:
  - 00README 
  - Opal.jar (the heart of Opal, a Java jar file)
  - opal (a shell script that runs Opal.jar with appropriate Java flags)
  - predict_structure.pl (a perl script that handles the job of calling
    psipred, and collating the results into a format recognized by Opal.jar) 

(2) To build a alignment, use one of the following commands:

       ./opal unaligned_seqs.fasta > alignment.fasta
       (or)
       ./opal --in unaligned_seqs.fasta --out alignment.fasta


(3) For further documentation, use two resources:
       ./opal --help
       00README distributed with Opal

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.