Archaeopteryx

Archaeopteryx visualizes, analyzes, and edits large, highly annotated phylogenetic trees to support evolutionary biology, comparative genomics, and phylogenomics research.

Key Features:

• Visualization: Advanced graphical representation of phylogenetic trees to explore relationships between organisms or genes.
• Analysis: Examination of tree structures, branch lengths, support values, and other attributes relevant to evolutionary inference.
• Editing: Direct modification of tree topology and annotations to update or refine phylogenetic hypotheses.
• Annotation Handling: Management of extensive node- and branch-level annotations including taxonomic names, gene identifiers, functional annotations, gene duplications, and speciations.

Scientific Applications:

• Comparative Genomics and Phylogenomics: Annotation and inspection of gene trees with genomic data to investigate genetic relationships and evolutionary histories.
• Evolutionary Studies: Association of taxonomic names and trait annotations with tree nodes and branches to study organismal relationships and evolutionary events.

Methodology:

Uses the phyloXML XML format with flexible "property" elements to encode annotations; the phyloXML schema is defined in XSD for data validation and interoperability; includes utilities for reading, writing, converting, and visualizing phyloXML-formatted data.