comparative-genomics

Name: comparative-genomics
Availability: InStock
Author: zongtingwei

Generates orthologs, synteny blocks, and evolutionary summaries from genome assemblies and annotations.

25|5|Updated Mar 22, 2026

Search Tags:#orthology #phylogenomics #evolutionary-analysis #genome-analysis #comparative-genomics #synteny

Ready to run

npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill comparative-genomics

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: comparative-genomics
Source: https://github.com/zongtingwei/Bioclaw_Skills_Hub/tree/main/skills/genomics-and-variation/comparative-genomics
Command: npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill comparative-genomics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This skill enables cross-genome analysis by generating ortholog tables, detecting conserved synteny, and summarizing evolutionary relationships across genomes.

Core Features & Use Cases

Orthology inference: identify orthologous gene sets across multiple genomes.
Synteny analysis: detect conserved gene order blocks and rearrangements.
Evolutionary summaries: produce ancestral state inferences and lineage-specific patterns.
Use Case: Compare genomes from related species to infer shared gene content and speciation signals.

Quick Start

Provide multi-genome assemblies and annotations to run the comparative-genomics workflow and generate ortholog tables and synteny outputs.

Frequently Asked Questions about comparative-genomics

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

FAQPage Schema

How do I identify orthologous gene sets across multiple genomes?▼

Orthology inference across multiple genomes is performed by generating ortholog tables from assembled genomes and annotations. This identifies conserved gene sets to distinguish shared gene content from lineage-specific changes.

What is synteny analysis and how does it detect conserved gene order?▼

Synteny analysis detects conserved gene order blocks and rearrangements across multiple taxa. By comparing assembled genomes, it identifies regions where gene order is preserved, revealing structural evolutionary relationships.

How do I infer ancestral states and lineage-specific changes from genome comparisons?▼

Inferring ancestral states and lineage-specific patterns requires comparing multiple taxa with assembled genomes and annotations. Evolutionary summaries are produced to reveal shared gene content, speciation signals, and ancestral gene order.

Can I run comparative genomics workflows using Python and standardized inputs?▼

Yes, comparative genomics workflows are Python-first and require standardized inputs of multi-genome assemblies and annotations. This modular approach ensures reproducible artifacts with clear QC and version tracking for cross-genome analysis.

What's the best way to compare related species genomes for evolutionary analysis?▼

The best way to compare related species genomes is providing assembled genomes and annotations to generate ortholog tables and synteny outputs. This cross-genome comparison infers shared gene content and speciation signals.

Do I need assembled genomes and annotations to detect synteny blocks?▼

Yes, assembled genomes and annotations are required to detect synteny blocks and generate orthologs. The comparative-genomics workflow needs these standardized inputs to identify conserved gene sets and lineage-specific changes.