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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.