This is the download page for a collection of protein sequence alignment benchmarks including BALIBASE v3, PREFAB v4, OXBENCH, and SABRE. These have been converted to a standard FASTA format that is convenient for further analysis. Accuracy scores for some selected methods are included to allow third party verification of my results.
 

This is tarball format, use tar -zxf bench.tar.gz to extract.

Alignment accuracies are computed using the qscore program.