Comparison of alignment software on BAliBASE v1.0. Alignment accuracy of multiple alignment programs compared to that of RetAlign as measured on BAliBASE v1.0 using the provided bali_score tool (SP and TC scores are both shown). RetAlign was run with sequence weighting on, a single guide tree iteration and with a reticular threshold of 200. FSA was run in maximum sensitivity mode. MAFFT was run with the -auto switch and ClustalW with the default settings.