Parameter Optimization Procedure
Developed by Robert C. Edgar.
Edgar RC., Optimizing substitution matrix choice and gap parameters for sequence alignment. BMC Bioinformatics, 2009 Dec 2;10:396.
This is the CLUSTALW command-line which gave an 8% improvement on BALIBASE v3.
clustalw -infile=filename -outfile=filename -align -matrix=VTML200 -gapopen=2.0 -gapext=0.1
I used version 2.0.9 of CLUSTALW.
All files are in "tarball" format, use tar -zxvf filename to extract files.