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 hosted by the Institute for Systems Biology, Seattle, US.
Treefam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.
AntiFam is a collection of hidden Markov models (HMMs) designed to identify spurious open reading frames (ORFs).
The iPfam database is no longer available.