These tab-delimited files give information about the families that appear in the FastHMM and FastBLAST results. FasthmmFamily2HMM is the mapping from the model name or HMM name (the entries in the raw hits) to the domain name in the *.gene3d.domains and *.superfam.domains files produced by FastHMM. It only includes the gene3d and superfam databases. PFam also has multiple HMMs for each family, but these are always named the same way. For example, for PF00244, the full-length model (at the time of writing) is PF00244.11, the fragment model is PF00244.11.fs, and the domains file will just have PF02225. DomainInfo has descriptive data on each family that appears in the *.domains files. Note that many entries are NULL. fileName has the name of the model (for PFam, the full-length model; for Gene3D and SUPERFAM this entry is absent as there are many values). COGInfo has a table with the COG number, the COG function code(s), the COG description, the gene name for the COG (or empty), the CDD identifier for the COG, and the length of the COG. The CDD identifier, of the form "gnl|CDD|30350", is what appears in the output of COGHits.pl and in the final tables from the first stage of FastBLAST.