eGPS Pathway Evolution Browser

A comprehensive Pathway evolutionary browser module suite for evolutionary analysis, multiple sequence alignment (MSA), phylogenetic tree construction, and pathway evolution visualization.

If you would like a bundled version that includes egps-base, egps-shell, and egps-pathway.evol.browser, please visit: https://github.com/yudalang3/eGPS2.1

Overview

eGPS Pathway Evolution Browser is a plugin module for the eGPS2 platform that provides 18 integrated bioinformatics tools. The module suite supports a complete workflow from gene sequence retrieval to phylogenetic tree construction and evolutionary distance analysis.

Key Features

• Pathway evolutionary browser: Interactive visualization with phylogenetic context of biological pathways
• Phylogenetic workflows: Build trees from MSA/MAF/distance matrices
• MSA toolkit: MAFFT alignment, trimming, and multi-format viewers
• Evolutionary distance analysis: Distance matrix computation and heatmap visualization

System Requirements

• Java: JDK 25 or higher
• Memory: Minimum 4GB heap (recommended: -Xmx8g)
• Platform: Windows, macOS, Linux

Optional Dependencies

• MAFFT: Required for multiple sequence alignment operations (external dependency)
  • The system can auto-detect MAFFT installation paths
  • Supports custom MAFFT configuration

Project Structure

egps-pathway.evol.browser/
├── src/module/                    # Source code modules
│   ├── ambigbse/                 # Ambiguous nucleotide tools
│   ├── evoldist/                 # Evolutionary distance (3 modules)
│   ├── evolview/                 # Evolution visualization (3 modules)
│   ├── multiseq/                 # Multiple sequence alignment (6 modules)
│   ├── pill/                     # Pathway illuminator
│   ├── treebuilder/              # Tree construction (4 modules)
│   ├── evoltrepipline/          # Shared pipeline components
│   └── [other utilities]/
├── dependency-egps/              # External JAR dependencies
├── docs/                         # Documentation (current)
├── src/api/rpython/             # External language bridge APIs for R/Python workflows
├── out/                          # Build output
├── CLAUDE.md                    # Developer guidance
└── compile.sh                   # Build script

Build & Compilation

Automatic Compilation

bash compile.sh

Manual Compilation

javac -d ./out/production/egps-pathway.evol.browser \
  -cp "dependency-egps/*" \
  $(find src -name "*.java")

Build Output

Compiled classes: ./out/production/egps-pathway.evol.browser

Running the Application

Development Mode

java -cp "out/production/egps-pathway.evol.browser:dependency-egps/*" \
  -Xmx12g @eGPS.args \
  egps2.Launcher4Dev

Production Mode

java -cp "out/production/egps-pathway.evol.browser:dependency-egps/*" \
  -Xmx12g @eGPS.args \
  egps2.Launcher

Launch Specific Module

java -cp "out/production/egps-pathway.evol.browser:dependency-egps/*" \
  -Xmx12g @eGPS.args \
  egps2.Launcher com.package.ModuleClassName

Modules

The suite contains 18 modules organized in 9 packages:

Sequence Tools

• ambigbse: Converts IUPAC ambiguous nucleotide codes (R, Y, M, K, S, W, H, B, V, D, N) to concrete sequences and reverse complements

Evolutionary Distance Analysis (3 modules)

• evoldist/gene2dist: Retrieve MSA from Ensembl/eGPS cloud sequences and compute evolutionary distance
• evoldist/msa2distview: Distance matrix calculation from MSA files (JC69, K2P, Tamura-Nei)
• evoldist/view: Heatmap visualization of evolutionary distance matrices

Evolutionary Visualization (3 modules)

• evolview/gfamily: Interactive gene family browser with phylogenetic trees and sequence structures
• evolview/moderntreeviewer: Modern phylogenetic tree viewer with multiple layouts
• evolview/pathwaybrowser: Biological pathway visualization with phylogenetic context

Multiple Sequence Alignment (6 modules)

• multiseq/aligner: MAFFT wrapper for fast multiple sequence alignment
• multiseq/alignerwithref: Reference-based MSA with MAFFT
• multiseq/alignment/trimmer: Trim MSA based on reference sequence
• multiseq/alignment/view: Interactive MSA viewer (ClustalW, FASTA, PHYLIP, NEXUS, etc.)
• multiseq/deversitydescriptor: Text-based alignment diversity metrics
• multiseq/gene2msa: Retrieve gene sequences from Ensembl/eGPS cloud and generate MSA

Pathway Tools

• pill: Pathway diagram drawing and editing tool (Pathway Illuminator)

Tree Construction (4 modules)

• treebuilder/gene2tree: Obtain MSA from Ensembl/UCSC and construct gene phylogenetic trees
• treebuilder/frommsa: Construct phylogenetic trees from multiple sequence alignments
• treebuilder/frommaf: Construct phylogenetic trees from MAF (Multiple Alignment Format) files
• treebuilder/fromdist: Construct phylogenetic trees from evolutionary distance matrices

Architecture

Module System

The application follows a modular architecture based on the IModuleLoader interface:

• Each module implements IModuleLoader interface
• UI panels extend ModuleFace abstract class
• Dynamic module loading and discovery

Module Versioning

All modules implement semantic versioning (Major.Minor.Patch):

@Override
public ModuleVersion getVersion() {
    return new ModuleVersion(1, 0, 0);
}

Dependency Management

The codebase maintains a Directed Acyclic Graph (DAG) architecture—no circular dependencies between modules.

Configuration

User configuration is stored in ~/.egps/:

• First-time launch: Creates configuration directory structure
• Module discovery: Automatic classpath scanning and plugin loading
• MAFFT integration: Auto-detection of MAFFT installation paths

External Language Integration

Java-side R and Python bridge entry points are centralized under src/api/rpython/.

Current examples include:

• API4R
• RlangInterfaceEGPS
• ModernTreeViewPyLauncher
• PathwayFamilyBrowserPyLauncher
• EvolTreeManipulator

Development

Logging

Important: Always use SLF4J Logger instead of System.out.println():

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

private static final Logger log = LoggerFactory.getLogger(MyClass.class);
log.info("Message: {}", value);
log.error("Error: {}", exception.getMessage());

UTF-8 Encoding

The system enforces UTF-8 encoding:

System.setProperty("file.encoding", "UTF-8")

HTML Documentation

For Swing JEditorPane support, use HTML 3.2 with CSS 1.0:

• No HTML5 semantic tags
• No CSS3 features (flexbox, grid, etc.)
• Use inline styles or <style> tags
• Use HTML tables for layout

Dependencies

Key libraries:

• Swing/SwingX - GUI framework
• Apache Commons (IO, Math3, Collections4, etc.)
• iText - PDF generation
• MigLayout - UI layout
• HTSJdk - Genomics file formats
• FastJSON - JSON processing
• SLF4J - Logging framework
• POI - Office file handling

See dependency-egps/ for complete list of JARs.

License

Licensed under the Apache License 2.0. See LICENSE file for details.

Platform Support

• Windows: Fully supported
• macOS: Fully supported
• Linux: Fully supported

Documentation

For detailed developer information, see:

• CLAUDE.md - Developer guidance and architecture details
• modules_we_have.md - Detailed module specifications
• docs/current/ - Current documentation
• src/api/rpython/README.md - R/Python bridge entry-point guide

Contributing

When developing or extending modules:

1. Implement IModuleLoader interface
2. Extend ModuleFace for UI
3. Follow semantic versioning in getVersion()
4. Maintain DAG architecture (no circular dependencies)
5. Use SLF4J for logging
6. Add HTML 3.2-compliant documentation

Contributors

• codex
• Claude

Support

For issues, questions, or contributions, please refer to the project documentation in docs/current/.

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Project: eGPS2 Pathway Evolution Browser Version: 2.2.0 Last Updated: 2026-01-01