etetoolkit

Load Newick format trees using ETE Toolkit's tree I/O functions, then render them with configurable 2D/3D layouts and custom styles via TreeStyle to produce publication-quality visualizations for research workflows.

ETE Toolkit supports loading, writing, and converting between Newick, NHX, PhyloXML, and NeXML formats, enabling seamless format transitions across phylogenetic analysis pipelines.

Use ETE Toolkit's evolutionary event detection and orthology inference functions to automatically identify duplication, speciation, and loss events, then extract orthologous gene groups across species.

Tree traversal and topology modification operations include loading, pruning, rooting, rerooting, and custom node manipulation to reshape phylogenetic structures for downstream analysis.

Link phylogenetic trees to NCBI taxonomy via ETE's NCBITaxa integration to annotate species names, validate taxonomic relationships, and enrich tree visualizations with standardized nomenclature.

Calculate pairwise distances, Robinson-Foulds distance metrics, and perform monophyly tests to quantify tree topology differences and validate evolutionary relationships.