We hope that the BRAliBase 2.1 reference alignments constitute a testing platform for developers, similarly as the BRAliBase II was already used for parameter optimization/training of MAFFT [25], MUSCLE [16,26], PROBCONSRNA [33], STRAL [36], and TLARA [39]. In the future we will try to provide a web interface, to which program authors may upload alignments created with their programs, that are than automatically scored and their performance plotted.