CAPT

CAPT visualizes phylogeny-based taxonomies by combining a phylogenetic tree view and a taxonomic icicle view to contextualize genomic and taxonomic information from next-generation sequencing data.

Key Features:

• Dual-View Visualization: Provides complementary phylogenetic tree and taxonomic icicle views for simultaneous examination of evolutionary relationships and hierarchical taxonomy.
• Taxonomic Icicle (Space-Filling) View: Represents taxonomic ranks (domain, phylum, class, order, family, genus, species) as space-filling partitions with sizes proportional to element counts.
• Linking and Brushing: Implements linking-and-brushing techniques to highlight correspondences and enable coordinated selection between the phylogenetic tree and icicle views.
• Integration of Genomic Context: Enriches clades in the phylogenetic view with genomic context derived from sequence and taxonomy data.
• Phylogeny-Based Taxonomy Representation: Presents taxonomy derived from phylogenetic relationships to support comparison and reconciliation of taxonomic frameworks.

Scientific Applications:

• Taxonomic Refinement: Integrates phylogenetic information with taxonomic hierarchies to support refinement of species and higher-level classifications.
• Phylogenetic Exploration: Enables exploration of complex phylogenetic trees to assess evolutionary relationships and clade composition.
• Taxonomic Validation against GTDB: Facilitates validation and case studies using scenarios derived from the Genome Taxonomy Database (GTDB).

Methodology:

CAPT applies interactive visualization with a dual-view phylogenetic tree and taxonomic icicle, uses linking-and-brushing between views, and enriches clades with genomic context.