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Table 3 Averaged ranks derived from Friedman rank sum tests for prank's gap parameter optimization.

From: An enhanced RNA alignment benchmark for sequence alignment programs

  ge
go 0.05 0.125 0.1875 0.25 0.375 0.5
0.0025 3.5 2.0 4.8 NA NA NA
0.00625 6.8 3.5 3.2 NA NA NA
0.00938 8.8 6.5 8.0 NA NA NA
0.0125 NA NA NA 8.2 11.0 13.5
0.01875 NA NA NA 12.8 12.5 15.8
0.025 NA NA NA 15.8 17.2 19.0
0.03125 NA NA NA 20.0 22.0 23.8
0.0375 NA NA NA 25.0 27.0 27.8
  1. Ranks (smaller values mean better performance) for each gap-open (go)/gap-extension (ge) value combination are averaged over all alignment sets with k {5, 7, 10, 15} sequences and APSI ≤ 80 %. The default option for PRANK version 1508b is given in bold-face. Values for sets k 2 and k 3 are missing because PRANK crashed repeatedly with these sets, but we needed all values to compute the Friedman tests.