The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).
The Dfam database is a collection of Repetitive DNA element sequence alignments, hidden Markov models (HMMs) and matches lists for complete Eukaryote genomes.
Treefam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.
The iPfam database is a catalog of protein family interactions, including domain and ligand interactions, calculated from known structures.
AntiFam is a collection of hidden Markov models (HMMs) designed to identify spurious open reading frames (ORFs).