Hongda-Zhao

Hongda-Zhao/bio-gene-to-reference-tree

Plugin Claude Code

Auditable bioinformatics Agent Skills maintained by Hongda Zhao.

Hongda-Zhao/bio-gene-to-reference-tree

Instructions file GitHub Copilot

Instructions for Hongda-Zhao/bio-gene-to-reference-tree, a project described as: Auditable agent skill for resolving protein queries, selecting references, and planning reproducible phylogenetic trees.

Hongda-Zhao/bio-gene-to-reference-tree

Skill Claude CodeCodex

Orchestrate this repository's end-to-end auditable protein or nucleotide gene-tree workflow. Use when a request spans several stages or the active stage is unclear; select one task adapter, then follow the canonical Skill and its review gates.

Hongda-Zhao/bio-gene-to-reference-tree

Skill Claude CodeCodex

Plan or review molecule-aware MSA, trimming sensitivity, and FastTree or IQ-TREE2 inference for an approved gene-tree reference set. Use for workflow Steps 6–8 while preserving separate alignment and inference approvals.

Hongda-Zhao/bio-gene-to-reference-tree

Skill Claude CodeCodex

Match a gene-tree task to available software and local, browser, SSH, or HPC environments without changing scientific decisions. Use for capability discovery, software alternatives, environment snapshots, route selection, or execution handoff planning.

Hongda-Zhao/bio-gene-to-reference-tree

Skill Claude CodeCodex

Resolve a protein, nucleotide, or CDS accession, local sequence, or name-plus-organism query and define its gene-tree objective. Use for molecule identity, provenance, exact taxonomy, analysis space, ingroup, or deliverable decisions before homolog discovery.

Hongda-Zhao/bio-gene-to-reference-tree

Skill Claude CodeCodex

Discover and review homolog or ortholog candidates, references, clustering, and outgroups for a protein or nucleotide gene tree. Use after query identity and scope are fixed and before sequence alignment begins.

Hongda-Zhao/bio-gene-to-reference-tree

Skill Claude CodeCodex

Create or review iTOL, ggtree or ggplot2, metadata, literature comparison, and final reporting for an approved gene tree. Use for workflow Steps 9–10 after inference artifacts exist.