Comparison of alignment software with fixed guide tree on BAliBASE v2.01 Refs [1–5]. Alignment accuracy of multiple alignment programs compared to that of RetAlign as measured on BAliBASE v2.01 Reference sets [1–5] when guide tree is fixed to MAFFT's output. Note that FSA does not need a guide tree but accuracy figures are shown for convenience. RetAlign was run with sequence weighting on, a single guide tree iteration and with a reticular threshold of 800. FSA was run in maximum sensitivity mode. MAFFT was run with the -auto switch and ClustalW with the default settings.