alterlab-etetoolkit

# ETE Toolkit Skill ## Overview ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analyze evolutionary events, visualize results, and integrate with biological databases for phylogenomic research and clustering analysis. ## ete3 or ete4? The examples in this skill and its references are written for **ete3 3.1.3**, which is still what most published pipelines import — but ete3 has had no release since May 2023, and **ete4 (4.4.0, Sept 2025)** is the maintained line. Port deliberately: the ete4 API is not drop-in. | ete3 | ete4 | |------|------| | `from ete3 import Tree` | `from ete4 import Tree` | | `Tree("t.nw", format=1)` | `Tree(open("t.nw"), parser=1)` — the keyword is `parser` | | `tree.iter_leaves()` / `get_leaves()` | `tree.leaves()` | | custom features via `node.add_feature()` | `node.props[...]` dictionary | | Qt-based `show()` / `render()` (needs PyQt5) | browser-based `explore()` with adaptive zoom, plus GTDB taxonomy support | Check which one is installed before writing code (`python -c "import ete4"`), and say which you targeted in the methods. ## When to Use - Parsing, traversing, or reformatting tree files (Newick / NHX / PhyloXML / NeXML) - Pruning, rooting, collapsing, or resolving polytomies in a tree - Detecting duplication/speciation events and inferring orthologs/paralogs from gene trees - Querying NCBI Taxonomy (taxid/name translation, lineages, taxonomy trees) - Producing public...