Pseudofam (http://pseudofam.pseudogene.org) is a database of pseudogene families 
based on the protein families from the Pfam database. It provides resources for 
analyzing the family structure of pseudogenes including query tools, statistical 
summaries and sequence alignments. The current version of Pseudofam contains 
more than 125,000 pseudogenes identified from 10 eukaryotic genomes and aligned 
within nearly 3000 families (approximately one-third of the total families in 
PfamA). Pseudofam uses a large-scale parallelized homology search algorithm 
(implemented as an extension of the PseudoPipe pipeline) to identify 
pseudogenes. Each identified pseudogene is assigned to its parent protein family 
and subsequently aligned to each other by transferring the parent domain 
alignments from the Pfam family. Pseudogenes are also given additional 
annotation based on an ontology, reflecting their mode of creation and 
subsequent history. In particular, our annotation highlights the association of 
pseudogene families with genomic features, such as segmental duplications. In 
addition, pseudogene families are associated with key statistics, which identify 
outlier families with an unusual degree of pseudogenization. The statistics also 
show how the number of genes and pseudogenes in families correlates across 
different species. Overall, they highlight the fact that housekeeping families 
tend to be enriched with a large number of pseudogenes.