Programs and options
The following program versions and options were used:
ClustalW : version 1.83[27]
default: -type=dna -align
gap-opt: -type=dna -align -pwgapopen=GO -gapopen=GO -pwgapext=GE -gapext=GE
subst-mat.: -type=dna -align -dnamatrix=MATRIX -pwdnamatrix=MATRIX
MAFFT : version 5.667[25]
default: fftns
default: ginsi
old: fftns --op 0.51 --ep 0.041
old: ginsi --op 0.51 --ep 0.041
MUSCLE : version 3.6[16,26]
-seqtype rna
PCMA : version 2.0[49]
POA : version 2[50]
-do_global -do_progressive MATRIX
prank : version 270705b – 1508b[29]
-gaprate=GR -gapext=GE
ProAlign : version 0.5a3[51]
java -Xmx256m -bwidth = 400 -jar ProAlign_0.5a3.jar
ProbConsRNA : version 1.10[33]
Prrn : version 3.0 (package scc)[52]