AnnoTree

AnnoTree provides integrated visualization and phylogenomic analysis of taxonomic, phylogenetic, and functional annotations across prokaryotic genomes to characterize gene family distributions and evolutionary processes.

Key Features:

• Data integration: Integrates taxonomy, phylogeny, and functional annotation data from over 27,000 bacterial and 1,500 archaeal genomes.
• Visualization of precomputed annotations: Visualizes millions of precomputed genome annotations mapped onto bacterial and archaeal phylogenies.
• Phylogenomic analysis of gene/protein families: Analyzes distributions of 28,311 gene/protein families and measures phylogenetic conservation, patchiness, and lineage-specificity.
• Identification of phylogenetic patchiness: Detects widespread phylogenetic patchiness and highlights traits involved in phage infection/defense, mobile elements, antibiotic resistance, and diverse metabolic enzymes that show frequent horizontal transfer.

Scientific Applications:

• Evolutionary history reconstruction: Enables examination of the evolutionary histories and phylogenomic distributions of prokaryotic genes and gene families.
• Horizontal gene transfer and gene flux analysis: Reveals patterns of gene gain, loss, and horizontal transfer across bacterial and archaeal lineages.
• Trait and functional evolution studies: Supports investigation of the distribution and lineage-specificity of traits related to phage interactions, mobile elements, antibiotic resistance, and metabolism.

Methodology:

Integration and visualization of comprehensive genomic, taxonomic, phylogenetic, and functional annotation data, with computation of phylogenetic conservation, patchiness, and lineage-specificity metrics for 28,311 gene/protein families.