etetoolkit

You can manipulate phylogenetic trees by loading Newick files, pruning branches, and rerooting nodes, then apply custom styling and faces to render publication-ready figures in PDF, SVG, or PNG formats.

Yes, you can detect evolutionary events like duplications and speciations by loading gene trees as PhyloTree objects and linking them to multiple sequence alignments to infer orthology and paralogy across taxa.

You can annotate phylogenetic trees with NCBI taxonomy by using the integrated NCBITaxa functionality to match tree leaf names, build lineages, and overlay taxonomic ranks directly onto the tree topology.

The best way to extract ortholog groups is by traversing the tree topology to identify speciation nodes, filtering out paralogous lineages, and isolating orthologous gene sets for downstream analysis.

Yes, ete3 supports end-to-end phylogenomics workflows by providing an integrated API that handles loading gene trees, detecting evolutionary events, extracting ortholog groups, and visualizing annotated results.

Handling tree manipulation errors during phylogenetic analysis is managed through the toolkit's robust error handling, which catches issues during tree loading, topology traversing, and alignment linking to prevent workflow failures.