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Table 5 Ranks determined by Friedman rank sum tests for all top-ranking programs.

From: An enhanced RNA alignment benchmark for sequence alignment programs

Program/Option

k2

k3

k5

k7

k10

k15

CLUSTALW (default)

8

7

8

8

7

7

CLUSTALW (optimized)

6

6

7

7

6

6

MAFFT (FFT-NS-2)

2

4

4

4

5

5

MAFFT (G-INS-i)

1

1

1

1

1

1

MUSCLE

3

3

3

2

2

2

PCMA

9

10

10

10

10

10

POA

7

8

9

9

9

9

PROALIGN

5

5

6

6

8

8

PROBCONSRNA

4

2

2

3

3

4

PRRN

10

9

5

5

4

3

  1. Programs were ranked according to BRALISCORE averaged over all alignment sets with k ∈ {2, 3, 5, 7, 10, 15} sequences and APSI ≤ 80 %. MAFFT (G-INS-i) is the top performing program on all test sets. For program versions and options see Methods.
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Algorithms for Molecular Biology

ISSN: 1748-7188