protein-phylogeny

What problem does it solve?

This Skill provides a reproducible protein phylogeny inference workflow by generating a complete .qmd analysis script that encodes input decisions, alignment and tree-building steps, and renders outputs in a structured directory.

Core Features & Use Cases

• Two-phase workflow: discuss the input and pipeline decisions with the user, then generate a ready-to-render Quarto script.
• Per-deliverable scripts: creates one .qmd script per major protein family or domain tree, consolidating all pipeline steps into a single reproducible document.
• Inputs, validation, and reporting: handles sequence validation, input paths, and a summary of results after rendering, including alignment and tree outputs.
• Use Case: build a phylogeny for a protein family across diverse taxa, from single-domain proteins to multi-domain proteins, using MAFFT for alignment and IQ-TREE for tree inference.

Quick Start

Discuss your input sequences with Claude to generate the .qmd script, then render it to produce outputs.