Evidente

Evidente integrates phylogenetic trees with genome-wide single-nucleotide polymorphism (SNP) data, sample metadata, and Gene Ontology (GO) enrichment to support interpretation of pathogen evolutionary relationships and functional genomic variation.

Key Features:

• SNP classification: Classifies SNPs into supporting and non-supporting categories relative to tree structures and maps their distribution across samples and clades.
• Phylogeny–SNP integration: Integrates phylogenetic trees with genome-wide SNP datasets and sample metadata to link genetic variation to clade structure.
• Metadata integration: Incorporates phenotypic and contextual sample metadata to connect genomic variants with sample attributes.
• GO-term enrichment analysis: Identifies over-represented genomic features encoded by Gene Ontology (GO) terms within specific clades of the phylogenetic tree.

Scientific Applications:

• Pathogen genomics: Applied to analyses of pathogens, including Treponema pallidum and Mycobacterium leprae, to explore evolutionary histories and genetic diversity.
• SNP-based phylogenetics: Applicable to any organism where SNP-based phylogenetic analysis is used to investigate lineage structure and variant distribution.

Methodology:

Integration of phylogenetic trees with comprehensive SNP datasets and sample metadata; classification of SNPs into supporting versus non-supporting relative to tree structures; and enrichment analysis to detect GO-term–encoded features over-represented within specific clades.