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+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+    <!-- Google tag (gtag.js) -->
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+    <title>Documentation - DNAnalyzer</title>
+    <meta name="description"
+        content="Comprehensive documentation for DNAnalyzer - Get started with our powerful DNA analysis tools and learn how to use all features.">
+
+    <!-- Stylesheets -->
+    <link rel="stylesheet" href="../style.css">
+    <link rel="stylesheet" href="docs.css">
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+        rel="stylesheet">
+
+    <!-- Favicon -->
+    <link rel="shortcut icon" href="../assets/icons/Icon_Dark_BG.svg" type="image/svg+xml">
+</head>
+
+<body>
+    <!-- Background effects -->
+    <div class="bg-gradient">
+        <div class="bg-blob bg-blob-1"></div>
+        <div class="bg-blob bg-blob-2"></div>
+    </div>
+
+    <div class="notification-banner">
+        <span>Exclusive WSSEF Preview: </span>
+        <span>&nbsp;Transformer Architecture in Epigenomics!</span>
+        <a href="https://epiclassify.dnanalyzer.org" target="_blank" class="notification-link">Explore Now</a>
+        <button class="notification-close" aria-label="Dismiss notification"></button>
+    </div>
+
+    <!-- Navbar -->
+    <nav class="navbar" id="navbar">
+        <div class="container navbar-container">
+            <a href="../index.html" class="logo">
+                <img src="../assets/icons/Icon_Dark_BG.svg" alt="DNAnalyzer Logo">
+                <span class="logo-text">DNAnalyzer</span>
+            </a>
+
+            <button class="mobile-toggle" id="mobileToggle" aria-label="Toggle navigation">
+                <i class="fas fa-bars"></i>
+            </button>
+
+            <ul class="nav-links" id="navLinks">
+                <li><a href="../index.html">Home</a></li>
+                <li><a href="../features/features.html">Features</a></li>
+                <li><a href="../analyzer/analyzer.html">Analyzer</a></li>
+                <li><a href="../server/server.html">Server</a></li>
+                <li><a href="docs.html" class="active">Docs</a></li>
+                <li><a href="../about/about.html">About</a></li>
+            </ul>
+
+            <div class="nav-buttons">
+                <a href="https://github.com/VerisimilitudeX/DNAnalyzer" class="btn btn-secondary btn-sm">
+                    <i class="fab fa-github btn-icon"></i> GitHub
+                </a>
+            </div>
+        </div>
+    </nav>
+
+    <!-- Documentation Layout -->
+    <div class="docs-layout">
+        <!-- Sidebar (Left) -->
+        <aside class="docs-sidebar" id="docsSidebar">
+            <div class="sidebar-header">
+                <h2>Documentation</h2>
+                <button class="mobile-close" id="closeSidebar">
+                    <i class="fas fa-times"></i>
+                </button>
+            </div>
+
+            <div class="sidebar-search">
+                <div class="search-input-wrapper">
+                    <i class="fas fa-search"></i>
+                    <input type="text" id="docsSearch" placeholder="Search documentation...">
+                </div>
+            </div>
+
+            <nav class="sidebar-nav">
+                <div class="nav-section">
+                    <h3>Getting Started</h3>
+                    <ul>
+                        <li><a href="#introduction" class="active">Introduction</a></li>
+                        <li><a href="#installation">Installation</a></li>
+                        <li><a href="#quick-start">Quick Start</a></li>
+                    </ul>
+                </div>
+
+                <div class="nav-section">
+                    <h3>Core Concepts</h3>
+                    <ul>
+                        <li><a href="#sequence-analysis">Sequence Analysis</a></li>
+                        <li><a href="#codon-detection">Codon Detection</a></li>
+                        <li><a href="#reading-frames">Reading Frames</a></li>
+                        <li><a href="#protein-prediction">Protein Prediction</a></li>
+                    </ul>
+                </div>
+
+                <div class="nav-section">
+                    <h3>Advanced Usage</h3>
+                    <ul>
+                        <li><a href="#server-setup">Server Setup</a></li>
+                        <li><a href="#api-reference">API Reference</a></li>
+                        <li><a href="#cli-usage">CLI Usage</a></li>
+                    </ul>
+                </div>
+
+                <div class="nav-section">
+                    <h3>Resources</h3>
+                    <ul>
+                        <li><a href="#faq">FAQ</a></li>
+                        <li><a href="#troubleshooting">Troubleshooting</a></li>
+                        <li><a href="#community">Community</a></li>
+                    </ul>
+                </div>
+            </nav>
+        </aside>
+
+        <!-- Content (Right) -->
+        <div class="docs-content">
+            <div class="docs-mobile-header">
+                <button class="sidebar-toggle" id="sidebarToggle">
+                    <i class="fas fa-bars"></i>
+                </button>
+                <h2>Documentation</h2>
+            </div>
+
+            <div class="docs-container">
+                <!-- Introduction -->
+                <section id="introduction" class="doc-section">
+                    <h1>Introduction to DNAnalyzer</h1>
+                    <p class="lead">DNAnalyzer is a powerful, privacy-focused DNA analysis tool using advanced machine
+                        learning models for accurate, on-device genomic analysis.</p>
+
+                    <p>This documentation will guide you through the installation, setup, and usage of DNAnalyzer for
+                        various DNA analysis tasks. Whether you're a researcher, educator, or bioinformatics enthusiast,
+                        you'll find comprehensive information on all of DNAnalyzer's capabilities.</p>
+
+                    <div class="info-box">
+                        <h3>Key Features</h3>
+                        <ul>
+                            <li><strong>Privacy-First Analysis:</strong> All processing occurs on your device, ensuring
+                                your genetic data never leaves your system.</li>
+                            <li><strong>Machine Learning Powered:</strong> Advanced ML algorithms provide exceptional
+                                accuracy in sequence analysis.</li>
+                            <li><strong>Comprehensive Tools:</strong> From basic sequence statistics to advanced protein
+                                prediction and promoter detection.</li>
+                            <li><strong>Open Source:</strong> DNAnalyzer is completely open source under the MIT
+                                License.</li>
+                        </ul>
+                    </div>
+
+                    <h2>System Requirements</h2>
+                    <p>Before getting started, ensure your system meets the following requirements:</p>
+
+                    <div class="code-block">
+                        <div class="code-header">
+                            <span class="code-label">System Requirements</span>
+                            <button class="copy-button">Copy</button>
+                        </div>
+                        <pre><code>- Operating System: Windows 10+, macOS 10.14+, or Linux (Ubuntu 18.04+)
+- Memory: 2GB RAM minimum (4GB+ recommended for large sequences)
+- Storage: 200MB for application, additional space for sequence files
+- Browser: Chrome 80+, Firefox 75+, Safari 13+, Edge 80+ (for web interface)
+- Java Runtime: Java 17+ (for server mode)</code></pre>
+                    </div>
+                </section>
+
+                <!-- Installation -->
+                <section id="installation" class="doc-section">
+                    <h1>Installation</h1>
+                    <p>DNAnalyzer can be installed and used in multiple ways depending on your needs and technical
+                        preferences.</p>
+
+                    <h2>Web Interface (No Installation)</h2>
+                    <p>The simplest way to use DNAnalyzer is through our web interface, which requires no installation:
+                    </p>
+                    <ol>
+                        <li>Visit <a href="../analyzer/analyzer.html">DNAnalyzer Web App</a></li>
+                        <li>Upload your DNA sequence files</li>
+                        <li>Select analysis options and get results</li>
+                    </ol>
+                    <p>The web interface runs entirely in your browser, ensuring your data never leaves your device.</p>
+
+                    <h2>Local Server Installation</h2>
+                    <p>For more advanced usage or batch processing, you can install DNAnalyzer as a local server:</p>
+
+                    <div class="tabs">
+                        <div class="tab-header">
+                            <button class="tab-button active" data-tab="windows">Windows</button>
+                            <button class="tab-button" data-tab="macos">macOS</button>
+                            <button class="tab-button" data-tab="linux">Linux</button>
+                        </div>
+
+                        <div class="tab-content active" id="windows">
+                            <ol>
+                                <li>Download the latest <a
+                                        href="https://github.com/VerisimilitudeX/DNAnalyzer/releases">DNAnalyzer
+                                        release</a> for Windows</li>
+                                <li>Extract the ZIP file to your preferred location</li>
+                                <li>Ensure Java 17 or newer is installed on your system</li>
+                                <li>Double-click on <code>dnanalyzer.bat</code> to start the server</li>
+                                <li>Access the interface at <code>http://localhost:8080</code> in your browser</li>
+                            </ol>
+                        </div>
+
+                        <div class="tab-content" id="macos">
+                            <ol>
+                                <li>Download the latest <a
+                                        href="https://github.com/VerisimilitudeX/DNAnalyzer/releases">DNAnalyzer
+                                        release</a> for macOS</li>
+                                <li>Extract the ZIP file to your preferred location</li>
+                                <li>Ensure Java 17 or newer is installed on your system</li>
+                                <li>Open Terminal and navigate to the extracted folder</li>
+                                <li>Run <code>chmod +x dnanalyzer.sh</code> to make the script executable</li>
+                                <li>Execute <code>./dnanalyzer.sh</code> to start the server</li>
+                                <li>Access the interface at <code>http://localhost:8080</code> in your browser</li>
+                            </ol>
+                        </div>
+
+                        <div class="tab-content" id="linux">
+                            <ol>
+                                <li>Download the latest <a
+                                        href="https://github.com/VerisimilitudeX/DNAnalyzer/releases">DNAnalyzer
+                                        release</a> for Linux</li>
+                                <li>Extract the archive to your preferred location</li>
+                                <li>Ensure Java 17 or newer is installed on your system</li>
+                                <li>Open Terminal and navigate to the extracted folder</li>
+                                <li>Run <code>chmod +x dnanalyzer.sh</code> to make the script executable</li>
+                                <li>Execute <code>./dnanalyzer.sh</code> to start the server</li>
+                                <li>Access the interface at <code>http://localhost:8080</code> in your browser</li>
+                            </ol>
+                        </div>
+                    </div>
+
+                    <h2>Building from Source</h2>
+                    <p>For developers or those who want the latest features, you can build DNAnalyzer from source:</p>
+
+                    <div class="code-block">
+                        <div class="code-header">
+                            <span class="code-label">Building from Source</span>
+                            <button class="copy-button">Copy</button>
+                        </div>
+                        <pre><code># Clone the repository
+git clone https://github.com/VerisimilitudeX/DNAnalyzer.git
+cd DNAnalyzer
+
+# Make the Gradle wrapper executable
+chmod +x ./gradlew
+
+# Build the project
+./gradlew clean bootJar
+
+# Run the server
+java -jar build/libs/DNAnalyzer.jar</code></pre>
+                    </div>
+                </section>
+
+                <!-- Quick Start -->
+                <section id="quick-start" class="doc-section">
+                    <h1>Quick Start Guide</h1>
+                    <p>This guide will help you quickly get started with DNAnalyzer's basic features.</p>
+
+                    <h2>Analyzing Your First DNA Sequence</h2>
+                    <p>Follow these steps to perform your first DNA sequence analysis:</p>
+
+                    <div class="steps">
+                        <div class="step">
+                            <div class="step-number">1</div>
+                            <div class="step-content">
+                                <h3>Upload a Sequence</h3>
+                                <p>Navigate to the <a href="../analyzer/analyzer.html">DNA Analyzer</a> page and upload
+                                    your FASTA or FASTQ file by dragging it to the upload area or clicking to browse.
+                                </p>
+                                <p><strong>Don't have a sequence file?</strong> Click "Import Sample" to use a
+                                    pre-loaded sample sequence.</p>
+                            </div>
+                        </div>
+
+                        <div class="step">
+                            <div class="step-number">2</div>
+                            <div class="step-content">
+                                <h3>Select Analysis Options</h3>
+                                <p>Choose which analysis features you want to run:</p>
+                                <ul>
+                                    <li><strong>Basic Analysis:</strong> Sequence length, GC content, base composition
+                                    </li>
+                                    <li><strong>Codon Analysis:</strong> Start codons, stop codons, reading frames</li>
+                                    <li><strong>Advanced Features:</strong> Coverage analysis, protein prediction,
+                                        promoter detection</li>
+                                </ul>
+                            </div>
+                        </div>
+
+                        <div class="step">
+                            <div class="step-number">3</div>
+                            <div class="step-content">
+                                <h3>Run Analysis</h3>
+                                <p>Click the "Start Analysis" button to process your sequence. The analysis time depends
+                                    on the sequence length and selected options.</p>
+                            </div>
+                        </div>
+
+                        <div class="step">
+                            <div class="step-number">4</div>
+                            <div class="step-content">
+                                <h3>Review Results</h3>
+                                <p>Examine the analysis results, which include visualizations, statistics, and detailed
+                                    information about your sequence.</p>
+                                <p>You can export the results in JSON, CSV, or text format for further processing or
+                                    documentation.</p>
+                            </div>
+                        </div>
+                    </div>
+
+                    <div class="info-box tip">
+                        <h3>Pro Tip</h3>
+                        <p>For large sequences (>1MB), consider using the local server installation for better
+                            performance and additional analysis options.</p>
+                    </div>
+                </section>
+
+                <!-- Sequence Analysis -->
+                <section id="sequence-analysis" class="doc-section">
+                    <h1>Sequence Analysis</h1>
+                    <p>DNAnalyzer provides comprehensive tools to analyze the basic properties of DNA sequences.</p>
+
+                    <h2>Base Composition Analysis</h2>
+                    <p>One of the fundamental analyses is determining the nucleotide composition of your DNA sequence:
+                    </p>
+
+                    <ul>
+                        <li><strong>Nucleotide Counts:</strong> Total count of A, T, G, C, and any other bases (N) in
+                            the sequence</li>
+                        <li><strong>Percentage Distribution:</strong> Proportion of each nucleotide type</li>
+                        <li><strong>Visualization:</strong> Interactive bar chart showing the distribution</li>
+                    </ul>
+
+                    <h2>GC Content Analysis</h2>
+                    <p>GC content is the percentage of nitrogenous bases in a DNA molecule that are either guanine (G)
+                        or cytosine (C):</p>
+
+                    <div class="code-block">
+                        <div class="code-header">
+                            <span class="code-label">GC Content Formula</span>
+                            <button class="copy-button">Copy</button>
+                        </div>
+                        <pre><code>GC Content (%) = (G + C) / (A + T + G + C) × 100</code></pre>
+                    </div>
+
+                    <p>GC content is important because:</p>
+                    <ul>
+                        <li>It affects DNA stability (higher GC content = more stable)</li>
+                        <li>GC-rich regions often indicate regulatory elements and gene-dense areas</li>
+                        <li>Different organisms have characteristic GC content ranges</li>
+                    </ul>
+
+                    <div class="info-box">
+                        <h3>Interpreting GC Content</h3>
+                        <ul>
+                            <li><strong>Low GC (< 40%):</strong> Common in AT-rich genomes like certain bacteria</li>
+                            <li><strong>Medium GC (40-60%):</strong> Typical of many eukaryotic genomes, including
+                                humans</li>
+                            <li><strong>High GC (> 60%):</strong> Often found in gene-rich regions and certain
+                                prokaryotes</li>
+                        </ul>
+                    </div>
+                </section>
+
+                <!-- More sections would continue here... -->
+
+                <!-- API Reference -->
+                <section id="api-reference" class="doc-section">
+                    <h1>API Reference</h1>
+                    <p>DNAnalyzer provides a RESTful API when running in server mode, allowing programmatic access to
+                        all analysis features.</p>
+
+                    <h2>API Endpoints</h2>
+                    <p>The following endpoints are available when the server is running:</p>
+
+                    <div class="api-endpoint">
+                        <div class="endpoint-method get">GET</div>
+                        <div class="endpoint-path">/api/v1/status</div>
+                        <div class="endpoint-description">
+                            <p>Check server status and version information</p>
+                            <h4>Response</h4>
+                            <div class="code-block">
+                                <pre><code>{
+  "status": "running",
+  "version": "1.0.0",
+  "uptime": "12h 34m 56s"
+}</code></pre>
+                            </div>
+                        </div>
+                    </div>
+
+                    <div class="api-endpoint">
+                        <div class="endpoint-method post">POST</div>
+                        <div class="endpoint-path">/api/v1/analyze</div>
+                        <div class="endpoint-description">
+                            <p>Analyze a DNA sequence file</p>
+                            <h4>Request</h4>
+                            <p>Form data with the following parameters:</p>
+                            <ul>
+                                <li><code>dnaFile</code> (required): The DNA sequence file to analyze</li>
+                                <li><code>options</code>: JSON string with analysis options</li>
+                            </ul>
+                            <h4>Response</h4>
+                            <div class="code-block">
+                                <pre><code>{
+  "sequence": {
+    "length": 1234,
+    "filename": "example.fa"
+  },
+  "basePairs": {
+    "counts": { "A": 300, "T": 310, "G": 320, "C": 304 },
+    "percentages": { "A": 24.3, "T": 25.1, "G": 25.9, "C": 24.7 },
+    "gcContent": 50.6
+  },
+  "analysis": {
+    // Additional analysis results based on options
+  }
+}</code></pre>
+                            </div>
+                        </div>
+                    </div>
+
+                    <div class="api-endpoint">
+                        <div class="endpoint-method post">POST</div>
+                        <div class="endpoint-path">/api/v1/base-pairs</div>
+                        <div class="endpoint-description">
+                            <p>Analyze base pair composition of a DNA sequence</p>
+                            <h4>Request</h4>
+                            <div class="code-block">
+                                <pre><code>{
+  "sequence": "ATGCATGCATGC"
+}</code></pre>
+                            </div>
+                            <h4>Response</h4>
+                            <div class="code-block">
+                                <pre><code>{
+  "counts": { "A": 3, "T": 3, "G": 3, "C": 3 },
+  "percentages": { "A": 25, "T": 25, "G": 25, "C": 25 },
+  "gcContent": 50
+}</code></pre>
+                            </div>
+                        </div>
+                    </div>
+
+                    <h2>Python Client Example</h2>
+                    <p>Here's a simple Python example to interact with the DNAnalyzer API:</p>
+
+                    <div class="code-block">
+                        <div class="code-header">
+                            <span class="code-label">Python</span>
+                            <button class="copy-button">Copy</button>
+                        </div>
+                        <pre><code>import requests
+
+# API base URL
+BASE_URL = "http://localhost:8080/api/v1"
+
+# Check server status
+response = requests.get(f"{BASE_URL}/status")
+print("Server status:", response.json())
+
+# Analyze a sequence
+with open("sequence.fa", "rb") as f:
+    files = {"dnaFile": f}
+    options = {
+        "sequence-length": True,
+        "gc-content": True,
+        "base-composition": True,
+        "start-codons": True,
+        "stop-codons": True
+    }
+    data = {"options": json.dumps(options)}
+    response = requests.post(f"{BASE_URL}/analyze", files=files, data=data)
+    
+    # Print results
+    result = response.json()
+    print(f"Sequence length: {result['sequence']['length']}")
+    print(f"GC content: {result['basePairs']['gcContent']}%")</code></pre>
+                    </div>
+                </section>
+
+                <!-- FAQ Section -->
+                <section id="faq" class="doc-section">
+                    <h1>Frequently Asked Questions</h1>
+
+                    <div class="faq-item">
+                        <div class="faq-question">
+                            <h3>Is my DNA data secure when using DNAnalyzer?</h3>
+                            <i class="fas fa-chevron-down"></i>
+                        </div>
+                        <div class="faq-answer">
+                            <p>Yes, DNAnalyzer is designed with privacy as a fundamental principle. All processing
+                                occurs locally on your device, and your DNA sequence data never leaves your system. In
+                                web mode, analysis runs directly in your browser, and in server mode, it runs only on
+                                your local machine. We don't collect, store, or transmit any of your sequence data.</p>
+                        </div>
+                    </div>
+
+                    <div class="faq-item">
+                        <div class="faq-question">
+                            <h3>What file formats does DNAnalyzer support?</h3>
+                            <i class="fas fa-chevron-down"></i>
+                        </div>
+                        <div class="faq-answer">
+                            <p>DNAnalyzer supports the following file formats:</p>
+                            <ul>
+                                <li>FASTA (.fa, .fasta)</li>
+                                <li>FASTQ (.fastq)</li>
+                                <li>Plain text (.txt) containing DNA sequences</li>
+                            </ul>
+                            <p>The sequences should contain only A, T, G, C, and N (unknown) nucleotides. Other
+                                characters will be treated as unknown bases.</p>
+                        </div>
+                    </div>
+
+                    <div class="faq-item">
+                        <div class="faq-question">
+                            <h3>How large of a sequence can DNAnalyzer handle?</h3>
+                            <i class="fas fa-chevron-down"></i>
+                        </div>
+                        <div class="faq-answer">
+                            <p>The size limitations depend on the mode of operation:</p>
+                            <ul>
+                                <li><strong>Web Interface:</strong> Up to around 5MB sequence files, depending on your
+                                    browser and device memory</li>
+                                <li><strong>Local Server:</strong> Can handle much larger sequences, typically up to
+                                    several hundred MB</li>
+                            </ul>
+                            <p>For very large genomes (e.g., human genome), we recommend using the local server
+                                installation with a machine that has at least 8GB of RAM.</p>
+                        </div>
+                    </div>
+
+                    <div class="faq-item">
+                        <div class="faq-question">
+                            <h3>Can DNAnalyzer analyze my 23andMe or Ancestry DNA data?</h3>
+                            <i class="fas fa-chevron-down"></i>
+                        </div>
+                        <div class="faq-answer">
+                            <p>Not directly in the current version. DNAnalyzer is designed to work with full DNA
+                                sequences rather than SNP genotype data from consumer genetics services. However, we're
+                                developing a feature to support genotype data analysis in an upcoming version.</p>
+                            <p>If you have raw data from these services, you would need to convert it to a suitable
+                                format before using it with DNAnalyzer.</p>
+                        </div>
+                    </div>
+
+                    <div class="faq-item">
+                        <div class="faq-question">
+                            <h3>Is DNAnalyzer open source?</h3>
+                            <i class="fas fa-chevron-down"></i>
+                        </div>
+                        <div class="faq-answer">
+                            <p>Yes, DNAnalyzer is completely open source under the MIT License. You can view, modify,
+                                and contribute to the code on our <a
+                                    href="https://github.com/VerisimilitudeX/DNAnalyzer">GitHub repository</a>.</p>
+                        </div>
+                    </div>
+                </section>
+
+                <!-- Community Section -->
+                <section id="community" class="doc-section">
+                    <h1>Community & Support</h1>
+                    <p>DNAnalyzer has an active community of users and developers. Here's how you can get involved and
+                        find support.</p>
+
+                    <h2>Getting Help</h2>
+                    <p>If you need assistance with DNAnalyzer, there are several resources available:</p>
+
+                    <div class="community-resources">
+                        <div class="resource-card">
+                            <i class="fab fa-discord"></i>
+                            <h3>Discord Community</h3>
+                            <p>Join our Discord server for real-time assistance and discussions about DNAnalyzer.</p>
+                            <a href="https://discord.gg/xNpujz49gj" class="btn btn-secondary btn-sm">Join Discord</a>
+                        </div>
+
+                        <div class="resource-card">
+                            <i class="fab fa-github"></i>
+                            <h3>GitHub Issues</h3>
+                            <p>Report bugs or request features through our GitHub issue tracker.</p>
+                            <a href="https://github.com/VerisimilitudeX/DNAnalyzer/issues"
+                                class="btn btn-secondary btn-sm">GitHub Issues</a>
+                        </div>
+
+                        <div class="resource-card">
+                            <i class="fas fa-book"></i>
+                            <h3>Documentation</h3>
+                            <p>Browse comprehensive guides and tutorials in our documentation.</p>
+                            <a href="docs.html" class="btn btn-secondary btn-sm">View Docs</a>
+                        </div>
+                    </div>
+
+                    <h2>Contributing</h2>
+                    <p>DNAnalyzer is an open-source project, and we welcome contributions from the community. There are
+                        many ways to contribute:</p>
+
+                    <ul>
+                        <li><strong>Code Contributions:</strong> Help improve DNAnalyzer by fixing bugs or adding new
+                            features</li>
+                        <li><strong>Documentation:</strong> Improve our guides, tutorials, and API documentation</li>
+                        <li><strong>Testing:</strong> Test DNAnalyzer and report issues or suggest improvements</li>
+                        <li><strong>Translations:</strong> Help translate DNAnalyzer into different languages</li>
+                    </ul>
+
+                    <p>To get started with contributing, please read our <a
+                            href="https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/CONTRIBUTING.md">contribution
+                            guidelines</a>.</p>
+
+                    <div class="info-box">
+                        <h3>Code of Conduct</h3>
+                        <p>We're committed to providing a welcoming and inclusive environment for all contributors.
+                            Please read and follow our <a
+                                href="https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/CODE_OF_CONDUCT.md">Code
+                                of Conduct</a>.</p>
+                    </div>
+                </section>
+            </div>
+        </div>
+    </div>
+
+    <!-- Footer -->
+    <footer class="footer">
+        <div class="container">
+            <div class="footer-grid">
+                <div class="footer-brand">
+                    <img src="../assets/icons/Icon_Dark_BG.svg" alt="DNAnalyzer Logo">
+                    <p>DNAnalyzer is a powerful, privacy-focused DNA analysis tool using cutting-edge machine learning
+                        models for accurate, on-device genomic analysis.</p>
+
+                    <div class="footer-social">
+                        <a href="https://www.twitter.com/DNAnalyzer_" class="social-link">
+                            <i class="fab fa-twitter"></i>
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+                    <h4>Product</h4>
+                    <ul>
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+                    </ul>
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+
+                <div class="footer-nav">
+                    <h4>Resources</h4>
+                    <ul>
+                        <li><a href="getting-started.md">Getting Started</a></li>
+                        <li><a href="citations.md">Citations</a></li>
+                        <li><a href="research/genes.md">Gene Research</a></li>
+                        <li><a href="samples/cli-arguments-examples.md">CLI Examples</a></li>
+                    </ul>
+                </div>
+
+                <div class="footer-nav">
+                    <h4>Community</h4>
+                    <ul>
+                        <li><a href="https://github.com/VerisimilitudeX/DNAnalyzer">GitHub</a></li>
+                        <li><a href="https://discord.gg/xNpujz49gj">Discord</a></li>
+                        <li><a href="contributing/CONTRIBUTING.md">Contributing</a></li>
+                        <li><a href="../CODE_OF_CONDUCT.md">Code of Conduct</a></li>
+                    </ul>
+                </div>
+            </div>
+
+            <div class="footer-bottom">
+                <div class="footer-copyright">
+                    Copyright &copy; Piyush Acharya 2025. DNAnalyzer is a fiscally sponsored 501(c)(3) nonprofit (EIN:
+                    81-2908499). MIT License.
+                </div>
+
+                <div class="footer-links">
+                    <a href="../LICENSE.md">License</a>
+                    <a href="../SECURITY.md">Security</a>
+                    <a href="../CITATION.cff">Citation</a>
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+</body>
+
+</html>
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