القائمة
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.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Use when an agent needs to call the VirusPrimerPro Agent API instead of the GUI, or prepare viral genome inputs for it: request/use API keys, download viral genomes from NCBI, install/run MAFFT, check and repair abnormal sequences, prepare phylogenetic trees/annotations, upload aligned FASTA/tree/GenBank files, poll runs, and fetch artifacts.
Use when an agent must define viral genotype, subtype, clade, lineage, target/background groups, or PhyloGuide groups from cited literature before primer or tNGS panel design.
Use when an agent must split tNGS or multiplex primer pairs into pools while minimizing primer-primer interaction risk and reporting pool overflows.
Use when an agent must evaluate primer candidates for wet-lab constraints such as length, GC, Tm, degeneracy, self-complementarity, pair complementarity, and amplicon size.
Use when an agent must select, filter, deduplicate, and document NCBI/GenBank/reference viral genomes before alignment, primer design, PhyloGuide, or tNGS panel design.
Use when an agent must batch-submit, poll, summarize, retry, or compare long-running VirusPrimerPro Agent API jobs without holding a long HTTP connection open.
| 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. |
Use this when prepare-phylo's deterministic p-distance neighbor-joining tree is insufficient for the species, dataset, or reporting standard.
python agentskill/scripts/advanced_phylogeny.py tool-plan \
--output phylo_tool_plan.json
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
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.