The files can be loaded by going to menu File->Open. The users are required to load a sequence file in the Fasta format and/or an associated annotation file, which is in NCBI ptt format. If the annotation file is not loaded, the users can still perform RNA LSS analysis but without annotation information. For bacterial genomes, the user can download fna and ptt files from NCBI FTP. For other sequence data, the users can also make their own files: sequence in the Fasta format and annotation file in NCBI ptt format for other sequence data. RnallViewer also supports the .gbk file format.