PanHOG

A phylogeny-aware toolkit for classifying and annotating Hierarchical Orthologous Groups (HOGs) in pangenomic datasets. It's a flexible command-line toolkit for classifying Orthofinder derived HOGs across multiple genomes in a pangenome-aware, phylogeny-informed context. It supports core/shell/private gene classification, heatmap visualization, pan-proteome generation, and saturation analysis. Now supports both command-line arguments and external configuration files.

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Key Features

• Global Pangenome Classification (--pan)
• Clade-Specific Analysis (--clade species1,species2)
• Pan-Proteome Construction (--proteome)
• Gene Variation Heatmap (--genevar)
• Bootstrapped Saturation Analysis (--saturation)
• Clade-based Saturation Analysis (--saturation-cladepair)
• Customizable via Config File (--config config.yaml)
• Pangene Integration for Gene Presence/Absence Analysis

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Documentation

• Install dependencies
• Configuration Guide - Detailed guide for configuring PanHOG with YAML files
• Pangene Integration Guide - Instructions for using the pangene integration module

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Basic Usage

python PanHOG.py --hog N0.tsv --fasta ./peptides/ --pan -o results/ -p run1_

With clade-specific analysis:

python PanHOG.py --hog N0.tsv --fasta ./peptides/ \
  --clade Arabis_alpina,ET_AA21_2,ET_AA6 --pan -o results/ -p cladeA_

With pan-proteome and gene variation heatmap:

python PanHOG.py --hog N0.tsv --fasta ./peptides/ \
  --proteome ALL --genevar ALL --zscore -o results/ -p viz_

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⚙️ Configuration File

You can now use a YAML config file to set advanced parameters like colors, markers, labels, and clade definitions.

Sample config.yaml

bootstrap: 10000
marker_core_clade1: "^"
marker_core_clade2: "s"
marker_pan_clade1: "^"
marker_pan_clade2: "s"
color_core_clade1: "#c0392b"
color_pan_clade1: "#f1c40f"
color_core_clade2: "#c0392b"
color_pan_clade2: "#3498db"
clade1:
  - Arabis_alpina
  - AA1
  - AA2
....
clade2:
  - Col_PEK
  - Col-CEN
....

Run using config:

python PanHOG.py --hog N0.tsv --fasta ./peptides/ --saturation-cladepair --config config.yaml

Any command-line flag will override the corresponding config value.

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Output Files

• core.HOGs.tsv, shell.HOGs.tsv, gt-specific.HOGs.tsv, single-copy.HOGs.tsv
• cloud.unassigned_genes.tsv
• private_genes_<species>.txt
• pan_proteome.fa
• genevar_heatmap.[png|pdf|svg]
• saturation_analysis.[png|pdf|svg]

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Recommendations

• Use --proteome to extract FASTA of shared pangenes.
• Use --saturation-cladepair for insight into core/pan genome expansion across defined clades.
• Use --genevar with --zscore for population-scale expansions or contractions.

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Contact & Citation

This tool is currently in beta. For questions, contributions, or citation requests, please contact the developer or include the GitHub link in your reference.

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Happy pangenomics with PanHOG! 🐼