TreeDyn

TreeDyn visualizes and annotates phylogenetic trees and other tree-based graphical representations to integrate meta-information such as taxonomic descriptions and gene functions.

Key Features:

• Dynamic visualization and editing: Provides dynamic visualization, editing, and analysis capabilities for phylogenetic trees and tree-based graphics.
• Meta-information integration: Integrates meta-information such as taxonomic descriptions and gene functions onto trees.
• Annotation capabilities: Projects texts or symbols onto leaf labels or nodes via manual pasting or annotation files.
• Query-based highlighting: Highlights graphical elements based on queries related to leaf labels, annotations, or selected graphical components.
• Targeted tree highlighting: Highlights targeted trees according to a source tree browsed by the user.
• Automation through scripting: Provides scripts to automate repetitive graphical tasks.
• Command-line interpreter and CGI integration: Includes a command-line interpreter and support for CGI scripts for scripted tree building and manipulation.
• Advanced export options: Exports graphics with HTML encapsulation and supports the TGF (Tree Graphics Format) for saving and restoring graphical analyses.
• Specialized research packages: Incorporates a library of packages tailored to specific research fields involving trees.

Scientific Applications:

• Biodiversity studies: Visualizes phylogenetic relationships and integrates taxonomic metadata for biodiversity analyses.
• Phylogenetic analysis: Supports tree-based analyses and comparative visualization of phylogenetic hypotheses.
• Structure/function investigations: Annotates and displays gene function or other functional metadata on tree structures.

Methodology:

Supports TGF for saving/restoring graphical analyses; projects annotations via manual pasting or annotation files; performs query-based and source-tree-based highlighting; provides scripting, command-line interpreter, and CGI support for automated and scripted tree building and manipulation; includes a library of research-specific packages.