TreeSearch

TreeSearch performs phylogenetic tree searches for morphological datasets using customizable optimality criteria (including profile parsimony) and explicit handling of inapplicable characters to improve parsimony-based inference.

Key Features:

• Custom Optimality Criteria: Supports profile parsimony and user-specified optimality criteria for tree searches.
• Handling Inapplicable Characters: Provides an explicit allowance for inapplicable character entries during tree search processes.
• Step Weights Flexibility: Supports tree searches using equal or implied step weights for scoring changes.
• Data Exploration Tools: Identifies and summarizes clusters of similar trees, maps the distribution of trees, and removes rogue taxa.

Scientific Applications:

• Evolutionary Biology: Enables reconstruction and comparison of morphological phylogenies to inform evolutionary hypotheses.
• Systematics: Supports evaluation of character-based hypotheses of relationships in systematic studies using morphological data.
• Taxonomy: Assists taxonomic inference by identifying phylogenetic relationships and detecting unstable (rogue) taxa in morphological datasets.

Methodology:

Performs tree searches under profile parsimony and user-specified optimality criteria, explicitly allows inapplicable character entries during search, and supports scoring with equal or implied step weights.