Fig. 3

General comparison of MSA matrix performance based on the average q-score \(\bar {q}\) per benchmark database. PFASUM MSA Matrices outperform the tested Standard MSA Matrices on all three benchmarks. PFASUM31 achieved the highest \(\bar {q}\) for BAliBASE 3.0 and SABmark 1.65, while VTML200 leads all matrices on the OXBench dataset. The red dotted line indicates the maximum \(\bar {q}\) separately for each benchmark