Phylogenetics and Sequence Analysis

RULE ZERO — Check for pre-computed results FIRST

Before following any instruction below, scan the data folder for:

• scogs_fungi.zip / scogs_animals.zip (BUSCO single-copy ortholog phylogenetics) → these contain the pre-computed alignments (*.faa.mafft.clipkit) and trees (*.faa.mafft.clipkit.treefile) from the original analysis. Use these directly with PhyKIT (see "BUSCO scogs questions" below). Re-running BUSCO → MAFFT → IQ-TREE from *.busco.zip files takes 1–6 hours AND produces slightly different numbers due to seed/version drift.
• *_executed.ipynb → read with tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}' and cite its cell outputs as the authoritative answer
• Pre-computed result files (CSV/TSV with names like *results*, *tree*, *phykit*, *saturation*, *treeness*) → read directly and report the requested value
• Canonical analysis scripts (analysis.R, run_*.py, find_*.R, *.Rmd) → execute as-is and read the output

Only follow this skill's re-analysis recipe below if none of the above exist. Re-running from raw data produces different numbers than the published answer and is much slower (often 5–10× turn count).

BUSCO scogs questions (multi-species phylogenomics)