What alignment and trimming tools are included in the workflow?

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

Which job schedulers are supported by this skill?

The skill supports SLURM, PBS/Torque, and local machine execution using GNU parallel, providing specific templates for each environment.

Can I use genomes from both local storage and NCBI?

Yes, the skill handles mixed inputs and provides scripts to query, download, and rename NCBI assemblies alongside your local files.

How does the skill handle software installation?

It generates a unified environment setup script that uses Conda or Mamba to install all necessary bioinformatics tools and dependencies.

Does it help with selecting evolutionary models?

Yes, it uses a systematic approach to recommend amino acid substitution models for IQ-TREE based on your dataset's taxonomic breadth and sequence characteristics.

Phylogenomics Workflow Generator

Name: Phylogenomics Workflow Generator
Author: brunoasm

bybrunoasm

•

数据科学与机器学习

Automates the generation of scheduler-aware phylogenomic workflows from genome assemblies using single-copy orthologs.

This skill provides specialized bioinformatics expertise for building comprehensive phylogenetic trees from genomic data. It manages the entire pipeline—from querying and downloading NCBI assemblies to performing BUSCO/compleasm analysis, ortholog extraction, alignment, and maximum likelihood tree inference. It is specifically designed to generate optimized scripts for SLURM, PBS/Torque, and local computing environments, ensuring reproducible and efficient phylogenomic analyses.

主要功能

01Advanced alignment trimming options including Aliscore and ALICUT

02Intelligent substitution model recommendation for IQ-TREE

03Hybrid input handling for local genome files and NCBI accessions

043 GitHub stars

05Automated workflow generation for SLURM, PBS, and local machines

06Integrated quality control and single-copy ortholog extraction scripts

使用场景

01Generating a species-level phylogeny from a collection of newly sequenced genome assemblies

02Scaling ortholog identification and alignment across high-performance computing clusters

03Systematically querying and downloading public genomic datasets for comparative genomics

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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