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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.