protein-phylogeny

To build a reproducible protein phylogeny pipeline, this Skill generates a Quarto script that encodes MAFFT alignment, optional trimming, and IQ-TREE tree inference steps, producing aligned sequences, guide trees, and final trees in a structured output directory.

Yes, MAFFT and IQ-TREE are used for phylogenetic inference across deep evolutionary distances. The workflow handles protein-domain phylogeny by validating input sequences, aligning them with MAFFT, and inferring trees with configurable IQ-TREE options.

To generate a reproducible phylogenetics analysis script, you need Python, Quarto, and the protein-phylogeny workflow. You discuss input sequences and pipeline decisions with Claude, which then creates a ready-to-render .qmd script.

The phylogeny workflow handles both single-domain and multi-domain protein families across diverse taxa. It creates one .qmd script per major protein family or domain tree, consolidating all pipeline steps into a single reproducible document.

The two-phase protein phylogeny workflow first discusses inputs and pipeline decisions with the user, then generates a Quarto script. Rendering this script validates sequences, runs alignment and tree inference, and reports results including aligned sequences and final trees.

A limitation of using a Quarto script for protein phylogeny inference is that it requires Python, Quarto, and the specific protein-phylogeny workflow environment to be pre-installed, as the generated .qmd script depends on these to render outputs successfully.