Bioinformatics Phylogenetics

ETE3 Library Standard Operating Procedure

PART 1: Core Tree Mechanics (ete3.Tree)

• Initialization Requirements: When loading a phylogeny from a string or file path, you must provide a format argument containing a single digit from 0 to 9. This digit dictates the specific interpretation of branch lengths, internal identifiers, and statistical support.
• Structural Iteration: To walk through the phylogeny, invoke the .traverse() method. You must supply a strategy argument set to exactly one of the following strings: preorder, postorder, or levelorder.
• Tip Extraction: To isolate only the outermost elements of the phylogeny, execute .get_leaves().

PART 2: Evolutionary Analysis (ete3.PhyloTree)

• Class Requirement: Ortholog and paralog identification cannot be performed on standard Tree objects. You are required to instantiate a PhyloTree for these tasks.
• Prerequisites for Event Detection: Prior to invoking .get_descendants_events(), you must verify two conditions:

1. The phylogeny possesses a valid root.
2. All tip elements are explicitly associated with species identifiers (achievable via a custom mapping dictionary or specific string-matching conventions).

PART 3: Taxonomic Mapping (ete3.NCBITaxa)

• Database Generation: Begin by instantiating NCBITaxa(). Be aware that the very first execution triggers an automatic download to construct an SQLite database on your local machine.
• Translation Commands: Extract taxonomic pathways and resolve identifiers by executing .get_lineage(taxid) and .get_taxid_translator().

PART 4: Strict Prohibitions (Critical Failure Points)

• Format Misalignment: Never supply an incorrect integer to the format parameter during initialization. Doing so causes the parser to erroneously assign statistical support numbers as internal node labels.
• Network Abuse: Never execute continuous web-based API calls to NCBI inside iterative loops. All repetitive taxonomic queries must be routed through the locally generated SQLite database.

Grounding (do this at runtime)

Do NOT answer precise facts (codes, identifiers, sections, current values) from memory — run the bundled script, and base the answer only on what it returns.

NOTICE

Based on the ETE Toolkit (Environment for Tree Exploration) documentation.