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bio-protein-clustering-pangenome

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Cluster proteins into orthogroups for pangenomes.

Data & Analytics#clustering#protein#phylogenomics#pangenome#orthogroups#presence-absence#paralogs
Authorfmschulz
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Cluster proteins into orthogroups and derive pan-genome matrices to support presence/absence analyses across many genomes.

Core Features & Use Cases

  • Orthogroup clustering with MMseqs2/ProteinOrtho to generate consistent gene families across genomes.
  • Pangenome statistics including core, accessory, cloud, and singleton partitions, plus single-copy orthologs for phylogenomics.
  • Use cases include large-scale bacterial pan-genome analysis, phylogenomic prep, and comparative genomics across numerous species.

Quick Start

Cluster proteins.faa into orthogroups using MMseqs2 or ProteinOrtho and generate a presence/absence matrix with core, accessory, and singleton classifications.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: bio-protein-clustering-pangenome
Download link: https://github.com/fmschulz/omics-skills/archive/main.zip#bio-protein-clustering-pangenome

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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