TreeFam

TreeFam is a database of phylogenetic trees of animal gene families. It aims to provide a comprehensive resource of orthologous and paralogous relationships between genes, focusing primarily on metazoan species. TreeFam distinguishes itself by its emphasis on a phylogenetic approach, using curated multiple sequence alignments and phylogenetic tree reconstruction to infer evolutionary relationships between genes.

The database is built around the concept of "families," where a family represents a group of genes descended from a single ancestral gene in the last common ancestor of animals. TreeFam uses a semi-automatic procedure for family construction, which involves sequence similarity searches, multiple sequence alignment, phylogenetic tree building, and manual curation. Expert curators review the trees, correct errors, and add information such as gene function and domain architecture.

The main goal of TreeFam is to provide a reliable and accurate source of orthology and paralogy information, which is essential for various applications in comparative genomics, evolutionary biology, and functional annotation. Users can search TreeFam by gene name, protein sequence, or keyword to find information about gene families, phylogenetic trees, and evolutionary relationships. The database also provides links to other relevant resources, such as sequence databases and functional annotation databases. The information in TreeFam can assist researchers in identifying orthologs in different species, predicting gene function, and understanding the evolutionary history of genes and genomes. TreeFam is periodically updated with new data and improved methodology.