advanced-phylogeny

name	advanced-phylogeny
description	Use when an agent needs a stricter or publication-grade phylogeny workflow for PhyloGuide, including tree/MSA validation, FastTree/IQ-TREE planning, and external-tree checks.

Advanced Phylogeny

Use this when prepare-phylo's deterministic p-distance neighbor-joining tree is insufficient for the species, dataset, or reporting standard.

Tool Plan

python agentskill/scripts/advanced_phylogeny.py tool-plan \
  --output phylo_tool_plan.json

Validate External Tree

Always validate the final Newick against the exact aligned FASTA IDs before phylo_guide submission:

python agentskill/scripts/advanced_phylogeny.py validate-tree \
  --msa aligned.normalized.fasta \
  --tree tree.newick \
  --output tree_validation.json

Optional External Trees

Run only when tools are installed:

python agentskill/scripts/advanced_phylogeny.py run-fasttree \
  --msa aligned.normalized.fasta \
  --output-tree fasttree.newick \
  --report fasttree_report.json

python agentskill/scripts/advanced_phylogeny.py run-iqtree \
  --msa aligned.normalized.fasta \
  --prefix iqtree_run \
  --bootstrap 1000 \
  --report iqtree_report.json

Use literature/curated taxonomy to define groups; a tree alone does not justify genotype labels.