ETE 4.4.0 review — September 30, 2026

PyPI and the official GitHub release catalogue still identify 4.4.0 as the current release. This skill targets that package. The installed core-tree, NCBI, GTDB, and PhyloTree source files were byte-identical to the official 4.4.0 tag during this review. The current documentation can disagree with released defaults; runtime behavior and tagged source resolve those differences.

Checked behavior

The isolated Python 3.13 suite exercises the bundled CLIs and synthetic scientific examples: parser selection, Newick/NHX/Nexus round trips, leaf identity, pruning with pairwise-distance preservation, rooting, RF, property caches, monophyly, ultrametric conversion, species-overlap events, reconciliation, alignment linkage, duplication splitting, and topology-only patterns. Tiny synthetic NCBI and converted-GTDB archives exercise actual SQLite construction, names/ranks/lineages, descendants, topology and annotation. The taxonomy fixtures reject unexpected requests.get() downloads.

Standalone runs also execute the documented preprocessing, metadata-join, midpoint, RF and offline-taxonomy examples. Qt SVG/PDF and SmartView PNG were rendered locally with their optional extras. These are small functional fixtures, not evidence of scientific accuracy for a real inferred tree.

Contracts that need particular care

• parser=0 is a valid explicit output choice. Never use a truthiness fallback when forwarding parser IDs.
• prune() accepts node objects. Resolve actual tips when internal labels can collide with leaf names; validating tip names and then passing strings still allows ambiguous resolution elsewhere in the tree.
• A zero maximum RF means normalization is undefined. The CLI emits JSON null, and rejects fewer than two common tips.
• set_midpoint_outgroup() computes the exact diameter midpoint. Selecting its containing edge with get_midpoint_outgroup() and using default set_outgroup() placement can produce a different root position.
• Support scale belongs to the input source. One percent and fractional one are different values; the color helper now requires a declared scale.
• Both CLI loaders reject nonfinite branch lengths and support. The released Newick parser accepts nan, inf, and overflowing exponents; these must not reach distance calculations, rendering, or JSON statistics.
• distance_matrix(squared=True) returns a square list of lists ordered by leaf iteration; it does not return labels or squared distances.
• render_sm() warns and returns if Selenium is absent. The helper checks dependencies and actual PNG bytes before reporting a saved artifact.
• The Qt PDF renderer selects A4 paper; drawing dimensions do not specify cropped page bounds. SmartView's narrow aligned panel can clip long titles. Inspect final artifacts rather than equating a successful write with layout QA.
• NCBITaxa(update=False) can still download when the database is missing. Pass the local archive during construction, or check that the pinned database exists before opening it offline. Retain its trusted traversal cache.
• A GTDB genome's sci_name may be its parent species. Use the original accession for genome identity.
• Alignment sequences are stored in leaf.props["sequence"], not a leaf.sequence attribute; check that all intended alignment names matched.

Public data access

These interfaces query local SQLite, not remote paginated JSON APIs. The released updater fetches public archives without credentials:

• NCBI: https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz; its .md5 sidecar returned a valid digest record during the review. ETE consults it for freshness of an existing archive, without verifying a fresh download. Its requests also lack timeouts and HTTP status checks.
• GTDB conversion: https://github.com/etetoolkit/ete-data/raw/main/gtdb_taxonomy/gtdblatest/gtdb_latest_dump.tar.gz. The official directory listing contained this archive but no .md5 sidecar; the sidecar returned 404. Pin an explicitly acquired release archive instead of treating this moving converted dump as a dated GTDB release.

No full public taxonomy database was downloaded. Real taxon-name examples remain illustrative until checked against the selected snapshot. External PAML models, large-tree performance, and remote SmartView deployments were not run. SmartView uses an unauthenticated local viewer; keep its loopback default.

Official sources

• Release 4.4.0
• PyPI release metadata
• Tree API
• Parser API
• PhyloTree API
• SmartView API
• Taxonomy tutorial
• Released core source
• Released NCBI source
• Released GTDB source
• Converted GTDB archive directory