Comparison of alignment software 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] using the provided bali_score tool (SP and TC scores calculated on all of the columns versus on columns containing features are all shown). 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.