Alignment Benchmark is 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.
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A paper is in submission. For now you can cite this URL: Edgar, R.C., http://www.drive5.com/bench.