The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).

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The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).

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The Dfam database is hosted by the Institute for Systems Biology, Seattle, US.

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Treefam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.

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AntiFam is a collection of hidden Markov models (HMMs) designed to identify spurious open reading frames (ORFs).

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The iPfam database is no longer available.