Notung

Notung integrates duplication/loss parsimony with gene-tree analyses to infer gene duplication and loss events and estimate duplication timings for evolutionary studies.

Key Features:

• Duplication/loss parsimony: Integrates duplication/loss parsimony into phylogenetic analyses to infer gene duplication and loss events from evolutionary trees.
• Rooted and unrooted tree support: Accepts and analyzes both rooted and unrooted gene trees.
• Duplication date inference: Automatically infers duplication dates from gene trees.
• Large-scale automation: Automates analysis to handle large sequence datasets and to explore alternative evolutionary hypotheses.
• Validation: Has been tested on previously published tree analyses and produced results consistent with original assessments.

Scientific Applications:

• Gene duplication analysis: Reconstructs histories and timings of gene duplication and loss to study genome evolution.
• Whole-genome duplication studies: Applied to investigate whole-genome duplications in genomes such as maize, yeast, and vertebrates.
• Evolutionary innovation research: Assesses the role of gene duplications in genetic functional innovation.
• Comparative phylogenetic hypothesis testing: Enables large-scale exploration and validation of alternative evolutionary hypotheses and published tree analyses.

Methodology:

Uses evolutionary gene trees together with duplication/loss parsimony to identify duplication and loss events and to estimate duplication dates for both rooted and unrooted trees.