Homologous vertebrate genes database (HOVERGEN)

Homologous vertebrate genes database (HOVERGEN) provides a curated resource of homologous genes across vertebrates for comparative sequence analysis, phylogenetic reconstruction, and inference of orthology and paralogy.

Key Features:

• Homologous Gene Selection: Selects sets of homologous genes across multiple vertebrate species for comparative analyses.
• Alignment and Tree Visualization: Supports visualization of multiple sequence alignments and phylogenetic trees.
• Orthology and Paralogy Analysis: Infers orthologs and paralogs by reconciling gene trees with species trees to identify speciation and duplication events.
• Tree Pattern Matching: Searches for gene families that match specified phylogenetic tree topologies with constraints on nodes and leaves.

Scientific Applications:

• Comparative Sequence Analysis: Compare sequences across species to assess functional conservation and divergence.
• Phylogenetic Studies: Reconstruct and interpret evolutionary relationships and lineage-specific adaptations using gene trees.
• Molecular Evolution Research: Analyze speciation and gene duplication events to investigate mechanisms driving genetic diversity and complexity.

Methodology:

Tree reconciliation comparing gene trees with species trees to infer speciation and duplication events; pattern-matching of phylogenetic tree topologies with node and leaf constraints; and visualization of multiple sequence alignments and phylogenetic trees for analysis.