SigTree

SigTree identifies phylogenetic branches whose operational taxonomic units (OTUs) show significant consensus changes in relative abundance across experimental conditions.

Key Features:

• Identification of Significant Phylogenetic Branches: Detects phylogenetic branches with consensus responses in OTU relative abundance across conditions.
• Integration with Phylogenetic Frameworks: Operates on phylogenetic trees of class phylo to map OTU-level signals to evolutionary lineages.
• Meta-analysis Methods: Synthesizes evidence across studies or experiments using meta-analysis techniques to increase robustness of detected branches.
• Regular Expression-based Data Handling: Uses regular expressions to parse and match tip labels and other data fields for flexible input handling.
• Visualization of Significant Branches: Produces visual representations of significantly responsive branches within phylogenetic trees.
• Multiple-Comparison Adjustment: Applies statistical adjustments, including control of false discovery rate, to account for multiple hypothesis testing.

Scientific Applications:

• Microbial ecology: Identifies clades responding to environmental changes or treatments to study community-level abundance shifts.
• Evolutionary biology: Contextualizes abundance changes within evolutionary lineages to infer phylogenetic patterns of response.
• Intervention and environmental impact studies: Supports analysis of treatment effects or environmental perturbations on OTU relative abundance across phylogenetic branches.

Methodology:

Integrates phylogenetic trees (class phylo) with data frames or matrices containing tip labels and OTU p-values; employs meta-analysis techniques, uses regular expressions for data handling, and applies multiple-comparison adjustments to control false discovery rates.