TreeVis

TreeVis generates two-dimensional layouts of complex tree structures derived from high-dimensional biological data to facilitate interpretation of phylogenetic relationships, transcriptomics-derived expression hierarchies, and protein interaction networks.

Key Features:

• Visualization Algorithm: A visualization algorithm tailored to handle tree structures derived from network-based analyses of biological data and produce clear, interpretable layouts.
• Two-Dimensional Layouts: Transforms high-dimensional or three-dimensional tree structures into two-dimensional layouts while preserving critical structural information such as node connectivity and branch-length relationships.
• Software Implementations: Implementations provided for MATLAB and R to enable integration into existing computational workflows.

Scientific Applications:

• Phylogenetics: Visualizing evolutionary relationships among species or genes using tree structures from phylogenetic analyses.
• Gene Expression Analysis: Interpreting complex transcriptomics-derived hierarchical patterns in gene expression data.
• Protein Interaction Networks: Representing and examining hierarchical organization within protein interaction networks produced by network-based analyses.

Methodology:

Converts high-dimensional tree structures into two-dimensional layouts using an algorithm that accounts for node connectivity, branch lengths, and overall structure complexity to produce an optimal, interpretable layout.