What is the Baez-Otter phylogenetic operad?

It is a mathematical framework where phylogenetic trees are viewed as a coproduct of the commutative semigroup operad (topology) and the non-negative real operad (metric lengths).

Can this skill help with Julia programming?

Yes, it provides specific implementations and schemas for Catlab.jl and ACSets.jl, enabling seamless integration with the Julia scientific computing ecosystem.

What is BHV treespace used for?

The Billera-Holmes-Vogtmann (BHV) treespace is used to measure the geometric distance between different evolutionary trees, helping researchers quantify biological divergence.

How does the Mathpix integration work?

The skill uses Mathpix-gem to scan PDFs for Newick strings or LaTeX tree environments (like TikZ or forest) and converts them directly into structured ACSet data.

Phylogenetic Operad & ACSet Tools

Name: Phylogenetic Operad & ACSet Tools
Author: plurigrid

byplurigrid

•

数据科学与机器学习

Models and analyzes phylogenetic trees using the Baez-Otter operad framework and Attributed C-Set (ACSet) schemas.

This skill implements the mathematical framework of Baez-Otter phylogenetic operads within Claude Code, allowing users to represent complex evolutionary trees as structured ACSets. By combining the 'Com' operad for topology and the '[0,∞)' operad for metric edge lengths, it provides a rigorous categorical foundation for biological modeling. It features automated tree extraction from academic papers via Mathpix, computes geodesics in Billera-Holmes-Vogtmann (BHV) treespace, and integrates with dendroidal infinity-operads for advanced research in computational biology and category theory.

主要功能

01BHV treespace geodesic and distance computation algorithms

02ACSet schema generation for Phyl = Com + [0,∞) operads

03Dendroidal nerve and infinity-operad integration for category theory

04Markov coalgebra implementation for evolutionary process modeling

05Automated tree extraction from PDF and LaTeX via Mathpix-gem

068 GitHub stars

使用场景

01Converting phylogenetic tree diagrams from research papers into machine-readable ACSet formats

02Analyzing evolutionary distance and tree paths in geometric BHV treespace

03Modeling Markovian state transitions on complex tree topologies using Catlab.jl

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add plurigrid/asi phylogenetic-operad-acset

For use in Claude.ai and ChatGPT

Download Skill