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Table 1 Program version numbers and command-line options

From: Accelerated large-scale multiple sequence alignment

Version Program Options
1.83 ClustalW -type = dna
2.04 Kalign --nuc
6.811 MAFFT --nuc
3.8.31a MUDISC -seqtype rna -maxiters 2
3.8.31a MUSCLE -seqtype rna -maxiters 2
2 POA -do_global -do_progressive
  1. MUDISC and MUSCLE additionally use the option "-termgaps full" on BRAliBase and "-termgaps ext" on MDSA when assessing alignment quality. MUDISC, MUFPGA, and MUSCLE use the options "-termgaps full -seqtype dna -gapopen 0 -center -300 -maxiters 2" for the performance test.