ViCTree

ViCTree performs automated taxonomic classification of viral protein sequences by retrieving sequences from NCBI GenBank and constructing maximum likelihood phylogenetic trees to support viral taxonomy.

Key Features:

• Automated sequence retrieval: Retrieves relevant protein sequences directly from NCBI GenBank for downstream analysis.
• Maximum likelihood phylogenetics: Constructs phylogenetic trees using a maximum likelihood approach from protein sequence alignments.
• Pairwise distance analysis: Computes pairwise distance data and places these distances in the context of the phylogenetic tree.
• Visualization component (ViCTreeView): Provides a JavaScript-based visualization of phylogenetic trees and associated pairwise distance data.
• Automated updating: Updates phylogenetic trees automatically as new sequence data are integrated.

Scientific Applications:

• Viral taxonomy and species discovery: Applied to the subfamily Densovirinae (family Parvoviridae) to classify sequences and identify six new insect virus species.
• Biodiversity and phylogenetic studies: Supports analysis of viral genetic diversity and evolutionary relationships using protein-sequence-based trees and distance metrics.

Methodology:

Automated retrieval of protein sequences from NCBI GenBank, computation of protein sequence alignments, construction of maximum likelihood phylogenetic trees, calculation of pairwise distances, and JavaScript-based visualization via ViCTreeView.