Are software dependencies difficult to install?

No, the skill generates a comprehensive environment setup script that uses Conda or Mamba to install all necessary tools and dependencies in a single step.

How does it handle substitution model selection for IQ-TREE?

It uses a systematic approach that fetches the latest IQ-TREE documentation and recommends specific models (e.g., LG, WAG, JTT) based on your data's taxonomic breadth and sequence type.

What alignment and trimming tools are supported?

The pipeline integrates MAFFT for alignment and offers multiple trimming options including Aliscore/ALICUT, trimAl, BMGE, and ClipKit.

Can I use my own local genome files instead of NCBI?

Yes, the workflow is designed to handle local genome files, NCBI accessions (GCA/GCF), or a mix of both types of input.

Does it support local machines or just HPC clusters?

The skill supports local execution using GNU Parallel, as well as SLURM and PBS/Torque schedulers for distributed computing on clusters.

BUSCO Phylogenomics Workflow Generator

Name: BUSCO Phylogenomics Workflow Generator
Author: brunoasm

bybrunoasm

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Data Science & ML

Generates comprehensive, scheduler-aware phylogenomics pipelines from genome assemblies using single-copy orthologs.

This skill automates the complex process of building phylogenetic trees from genomic data by leveraging BUSCO or compleasm to identify single-copy orthologs. It guides users through the entire bioinformatics lifecycle—from querying and downloading NCBI assemblies to alignment, trimming, and maximum likelihood tree inference—while providing environment-specific scripts for SLURM, PBS, or local execution. It is particularly useful for researchers needing reproducible, high-throughput workflows that handle everything from quality control to final species tree estimation.

Key Features

01Automated NCBI genome discovery and batch downloading using taxon names or accessions.

02Intelligent IQ-TREE substitution model recommendations based on taxonomic scope.

03Unified environment setup with Conda/Mamba for all required bioinformatics tools.

04Scheduler-aware script generation for SLURM, PBS, and local systems using GNU Parallel.

05End-to-end pipeline management including QC, ortholog extraction, alignment, and concatenation.

063 GitHub stars

Use Cases

01Automating ortholog identification and quality control for comparative genomics research.

02Constructing large-scale species trees from raw genome assemblies or NCBI data.

03Generating reproducible phylogenomics pipelines for high-performance computing (HPC) clusters.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add brunoasm/my_claude_skills phylo_from_buscos

For use in Claude.ai and ChatGPT

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