Hogenom_tree

Hogenom_tree performs comparative sequence analysis and phylogenetic inference to identify orthology and paralogy across gene families using the HOBACGEN, HOVERGEN, and HOGENOM databases.

Key Features:

• HOBACGEN, HOVERGEN, HOGENOM databases: Store sequences, multiple alignments, and phylogenetic trees of homologous genes.
• Tree reconciliation algorithm: Compares gene trees with species trees to infer speciation and duplication events and distinguish orthology from paralogy.
• FamFetch unordered tree pattern matching: Matches user-defined tree topologies with constraints on nodes and leaves against phylogenetic trees to detect gene families exhibiting specified patterns.
• Automated ortholog/paralog search: Executes automated searches for orthologs and paralogs within the databases using reconciliation and pattern-matching methods.

Scientific Applications:

• Comparative genomics: Analyze genome function and evolution through comparative sequence analysis.
• Gene family evolution: Reconstruct evolutionary histories by identifying speciation and duplication events in gene families.
• Orthology and paralogy detection: Differentiate orthologs from paralogs to support functional inference across species.
• Phylogenetic pattern discovery: Identify gene families that match specific tree topologies or evolutionary scenarios.
• Conserved function identification: Detect genes with conserved functions across species via homology relationships.

Methodology:

Databases store sequences, multiple alignments, and phylogenetic trees; a tree reconciliation algorithm compares gene trees with species trees to infer speciation and duplication events; FamFetch performs unordered tree pattern matching with constraints on nodes and leaves to find gene families matching specified topologies.