Sep 24th 2009 Benchmark collection
Now PREFAB v4.0 has been combined with a number of existing and new (so far unpublished) benchmarks in the Benchmark Collection.

 

PREFAB Protein Reference Alignment Benchmark

PREFAB is a database designed for testing multiple sequence alignment methods.

Citing PREFAB
Please cite the MUSCLE paper for PREFAB:

Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.

Current version 4.0, posted March 2005.

Download PREFAB 4.0.

The scoring software, qscore, is available here.

Obsolete versions
 Download PREFAB 1.0.
Download PREFAB 2.0.
Download PREFAB 3.0