For all the programs, unaligned sequence files can be in FASTA, Genbank, EMBL, or SwissProt format, as well as a few other common file formats. The programs automatically detect what format the file is in and whether the sequences are DNA, RNA, or protein. Aligned sequence files can be in GCG MSF format or SELEX format. SELEX format is a simple format of one line per sequence, containing the name first, followed by the aligned sequence. MSF and SELEX alignment files can also be used where unaligned format files are required; the sequences will be read in and their gaps removed. Full specifications of these file formats and the other formats recognized by the HMM package are in the File Formats section of the appendix.
If you forget the command-line syntax or available options of any of the programs, you can type the name of the program with no other arguments and get a short help message. If you also include option -h, you get version info as well (the software version number is helpful if you report bugs or other problems to me).
The programs work on RNA, DNA, and protein sequence. They automatically detect what your sequences are. The behavior of the programs when a nucleic acid model is used to analyze protein sequences, or vice versa, is undefined. Certain other situations may arise (trying to search the ``complementary strand'' of a protein database, for example) that are nonsensical in certain contexts. Be forewarned. If you're lucky, the software may issue a snide warning to you if you try to do something nonsensical, but quite possibly it will crash.
Some of the programs may have experimental options listed for their usage. These options are separated from the rest and annotated as experimental. Usually, supported options are in small letters, and experimental options are in capitals. Use experimental options at your own risk. They're my mechanism for trying out new ideas, and I don't always support them adequately. The ones that work slowly migrate to supported small letter options, and the ones that don't eventually disappear.