TreeFam

TreeFam curates phylogenetic trees of animal gene families and assigns orthologs and paralogs to provide evolutionary histories for animal gene families.

Key Features:

• Manual curation: As of release 1.1, TreeFam contains manually curated phylogenetic trees for 690 gene families.
• Automatic tree generation: TreeFam includes automatically generated phylogenetic trees for 11,646 additional gene families.
• Seed alignments: Curated entries are based on seed alignments and phylogenetic trees.
• Gene content: The resource encompasses over 128,000 genes from nine fully sequenced animal genomes.
• UniProt integration: TreeFam incorporates more than 45,000 other animal protein sequences sourced from UniProt.
• Ortholog and paralog assignments: The database provides reliable assignments of orthologs and paralogs for gene families.
• Genome coverage: TreeFam represents approximately 40–85% of the protein-coding genes encoded in the included fully sequenced animal genomes.
• Methodological inspiration: The curation approach draws methodological inspiration from Pfam.

Scientific Applications:

• Comparative genomics: Provides phylogenetic trees and orthology relationships to support cross-species genomic comparisons.
• Evolutionary biology: Enables reconstruction of gene family evolutionary histories and the study of paralogy and speciation events.
• Functional annotation: Supports functional annotation by transferring functional inference via orthologous relationships.

Methodology:

Entries are generated from seed alignments and phylogenetic tree reconstruction, combining manual curation (690 families) and automatic tree generation (11,646 families), with an approach inspired by Pfam.