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Table 3 Comparison with MACSE multiple alignments benchmark

From: Aligning coding sequences with frameshift extension penalties

fs_open_cost fse0 fse (−1) fse (−0.5) fse (−0.2) macse_p needlenuc needleprot
-10 79.58 (1404) 79.40 (1364) 79.52 (1415) 79.58 (1433) 77.17 (1076) 50.95 (255) 78.82 (972)
-20 79.68 (1550) 79.68 (1526) 79.65 (1558) 79.67 (1552) 78.29 (1389)   
-30 79.75 (1558) 79.47 (1529) 79.60 (1546) 79.63 (1547) 47.35 (742)   
  1. Percentage of nucleotides aligned with the same partner as in the benchmark alignments induced by the MACSE multiple alignments, for each method for varying fs_open_cost (\(-10\), \(-20\) and \(-30\)) and fs_extend_cost (\(-1\), \(-0.5\) and \(-0.2\)). In each case, the number of CDS pairs with an alignment that presents the highest similarity with the corresponding benchmark alignment as compared to the other methods is given in parenthesis. The best results are indicated in italics