bio-phylogenomics

Extract marker genes, generate alignments, and infer phylogenetic trees.

7|1|Updated Feb 2, 2026

Search Tags:#alignment #marker-genes #phylogenomics #phylogenetic-trees #iq-tree #ete-toolkit

Ready to run

npx skills add https://github.com/fmschulz/omics-skills --skill bio-phylogenomics

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: bio-phylogenomics
Source: https://github.com/fmschulz/omics-skills/tree/main/skills/bio-phylogenomics
Command: npx skills add https://github.com/fmschulz/omics-skills --skill bio-phylogenomics

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Marker gene phylogenomics workflows are laborious and prone to inconsistency; this skill provides a reproducible framework to extract marker genes, align them, and infer robust phylogenetic trees.

Core Features & Use Cases

Marker gene extraction, alignment, and trimming following project-standard workflows.
Phylogenetic tree inference using validated methods with bootstrap support and post-processing.
Use Case: Build cross-taxon phylogenies from marker genes to infer species relationships.

Quick Start

Provide your marker gene set and run the workflow to produce alignments and phylogenetic trees.

Frequently Asked Questions about bio-phylogenomics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I automate marker gene alignments and phylogenetic tree inference?▼

Automate marker gene alignments and phylogenetic tree inference by providing your input genomes to extract sequences, generate standardized alignments, and infer publication-ready phylogenies with validated bootstrap support.

Can I build cross-taxon phylogenies from marker genes for bacteria and eukaryotes?▼

Yes, you can build cross-taxon phylogenies from marker genes for bacteria, archaea, and eukaryotes. The workflow handles single-marker and multi-marker datasets across diverse taxa to infer species relationships.

What's the best way to ensure reproducible phylogenomic workflows?▼

Ensure reproducible phylogenomic workflows by using standardized frameworks that enforce input validation, model selection, bootstrap support assessment, and robust post-processing to maintain traceable provenance across your phylogenetic trees.

Does this phylogenomics workflow use IQ-TREE and ete-toolkit for post-processing?▼

Yes, the phylogenomics workflow uses IQ-TREE and ete-toolkit for tree inference and robust post-processing, applying validated methods with bootstrap support to generate publication-ready phylogenies.

How do I generate publication-ready phylogenetic trees from input genomes?▼

Generate publication-ready phylogenetic trees from input genomes by extracting marker gene sequences, aligning and trimming them, and applying quality gates with model selection and bootstrap support assessment.

When do I need quality gates and model selection in phylogenomic tree inference?▼

You need quality gates and model selection in phylogenomic tree inference when building robust cross-taxon phylogenies from marker genes, ensuring traceable provenance and publication-ready results with validated bootstrap support.