NAR Molecular Biology Database Collection entry number 875
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.

Database Description

TreeFam (Tree families database) is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families.

TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.

TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.

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