bio-phylogenomicslisted

# Bio Phylogenomics Build marker gene alignments and phylogenetic trees. ## Instructions 1. Extract marker genes or SSU rRNA sequences. 2. Align with MAFFT v7.5+ and trim with trimAl v1.4 (or ClipKIT when phylogenetically-informed trimming is preferred). 3. Build ML trees with support values. Choose by objective first, then leaf count: - Exploratory placement, benchmark iterations, reference-set screening, or any time-bounded analysis: use VeryFastTree v4.0 first, even below ~2,000 taxa. Prefer `VeryFastTree -boot 1000 -threads <n> < alignment.faa > tree.nw` for proteins and add `-nt` for nucleotide alignments. - Final or publication-quality trees up to ~2,000 taxa: IQ-TREE v3 (v3.1.2+) for comprehensive model selection, MAST/GTRpmix, UFBoot/SH-aLRT, and defensible final inference. - Above ~2,000 taxa, or when memory/runtime is uncertain: VeryFastTree v4.0 (multi-threaded, SIMD, `-disk-computing` for very large trees). - Use `iqtree3 -fast` only when VeryFastTree is unavailable or a project explicitly requires IQ-TREE-compatible exploratory output; record that fallback in the report. 4. Post-process trees with ETE v4 (`ete4`): - Compute tree statistics (branch lengths, distances, topology metrics). - Root, prune, or collapse nodes as needed. - Filter by bootstrap support. - Add taxonomic or trait annotations. - Generate publication-quality visualizations. 13. Use the literature-derived analysis playbook to choose markers, reference sampling, root