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Table 4 Matrices ranging by alignment quality

From: The ranging of amino acids substitution matrices of various types in accordance with the alignment accuracy criterion

Local Alignment Global Alignment
120 PAM Balibase 120 PAM Balibase
PAM250 0.7645 Gonnet_p 0.6386 PAM250 0.8283 Gonnet250 0.6567
Gonnet_p 0.7599 Gonnet250 0.5941 Gonnet250 0.8083 Pfasum050 0.6553
Gonnet250 0.7490 MIQS 0.5904 VTML250 0.8064 VTML250 0.6515
VTML250 0.7485 Pfasum050 0.5879 MIQS 0.8005 MIQS 0.6499
MIQS 0.7315 VTML250 0.5872 Pfasum050 0.7977 Optima 0.6489
Pfasum050 0.7167 Optima 0.5866 Optima 0.7869 Gonnet_p 0.6412
Optima 0.6888 PAM250 0.5624 Gonnet_p 0.7800 PAM250 0.6275
  1. Matrices are presented that show the best quality of local and global alignment on the 120 PAM and Balibase test sets. Ranking in descending order is based on the average value of the Accuracy and Confidence parameters