etetoolkit

To visualize a phylogenetic tree, load your Newick file and render it as a publication-quality PDF, SVG, or PNG. Custom node styling and faces are supported via TreeStyle and NodeStyle for high-quality outputs.

You infer orthologs and paralogs by analyzing gene trees to detect duplication and speciation events. This allows you to split gene families based on their evolutionary events for accurate orthology detection.

Yes, you can measure phylogenetic tree topology differences using the Robinson-Foulds metric. The toolkit computes distances and compares topological variations between multiple phylogenetic trees.

Yes, ete3 supports reading and writing multiple tree formats including Newick, NHX, PhyloXML, and NeXML. This enables seamless I/O operations for loading, manipulating, and saving phylogenetic tree structures.

The best way to annotate a species tree with NCBI taxonomy is by using the NCBITaxa operations. This integrates taxonomic data directly into your tree, enabling taxonomy-aware annotation and visualization.

To compute cluster quality metrics like the silhouette score for a dendrogram, use the ClusterTree functionality. This analyzes hierarchical clustering dendrograms and calculates metrics including the Dunn index and silhouette score.