etetoolkit

To extract ortholog groups from a phylogenetic tree, you can load a gene tree using PhyloTree to identify duplications and speciations, then isolate ortholog sequences for downstream analysis. This programmatically detects evolutionary events to streamline orthology inference.

You can annotate phylogenetic trees with NCBI taxonomy data by connecting the tree topology to the NCBI taxonomy database. This integration allows you to build and annotate trees programmatically, mapping species information directly onto your phylogenetic structures.

Yes, you can generate publication-quality phylogenetic tree visualizations using Python by rendering trees into PDF, SVG, or PNG formats. The toolkit provides styling options to produce high-resolution figures suitable for academic publications.

Comparing phylogenetic tree topologies involves calculating Robinson-Foulds distances and applying clustering metrics to evaluate similarities. This approach supports consensus analysis and tree comparisons to determine topological differences across gene trees.

Reading and manipulating Newick and NHX formats involves using tree I/O functionalities to load, navigate, prune, and reroot phylogenetic structures. This allows you to programmatically traverse and modify tree topologies for complex phylogenomic workflows.

Yes, ete3 supports tree rerooting and pruning to handle large-scale phylogenomic workflows. You can programmatically navigate loaded tree topologies to prune specific branches or reroot structures, streamlining complex phylogenetic tree manipulation tasks.