diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
new file mode 100644
index 0000000..ccb8887
--- /dev/null
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,107 @@
+## Summary
+
+<!-- Provide a brief 1-2 sentence summary of what this PR does -->
+
+
+
+---
+
+## Features
+
+<!-- 
+  List new features or enhancements added in this PR.
+  Delete this section if not applicable.
+  
+  Format:
+  - Brief description of the feature
+  - Another feature added
+-->
+
+- 
+
+---
+
+## Bug Fixes
+
+<!-- 
+  List bugs that are fixed by this PR.
+  Delete this section if not applicable.
+  
+  Format:
+  - Fixed issue where X happened when Y
+  - Resolved crash when doing Z
+-->
+
+- 
+
+---
+
+## Breaking Changes
+
+<!-- 
+  List any changes that break backwards compatibility.
+  Delete this section if not applicable.
+  
+  Format:
+  - Changed `--old-flag` to `--new-flag`
+  - Removed deprecated function `oldFunction()`
+  - Changed output format from X to Y
+-->
+
+- 
+
+---
+
+## Checklist
+
+- [ ] I have updated the `version` in `build.gradle.kts` (REQUIRED - see below)
+- [ ] I have tested these changes locally
+- [ ] I have added/updated tests for new functionality
+- [ ] I have updated documentation (if applicable)
+- [ ] Breaking changes are clearly documented above
+
+---
+
+<!--
+
+==== IMPORTANT: VERSION UPDATE REQUIRED
+
+Before this PR can be merged, you MUST update the version in
+build.gradle.kts to be HIGHER than the current released version.
+
+The PR will fail the version check if you don't update it!
+
+Example in build.gradle.kts:
+  version = "0.2.0"  // Update this to be higher than current release
+
+Semantic Versioning Guide:
+  - MAJOR version: Breaking changes (e.g., 1.0.0 -> 2.0.0)
+  - MINOR version: New features, backwards compatible (e.g., 1.0.0 -> 1.1.0)
+  - PATCH version: Bug fixes (e.g., 1.0.0 -> 1.0.1)
+
+
+==== PR DESCRIPTION GUIDELINES
+
+1. SUMMARY
+   - Keep it concise (1-2 sentences)
+   - Focus on WHAT changed and WHY, not HOW
+
+2. FEATURES / BUG FIXES / BREAKING CHANGES
+   - Use bullet points for each item
+   - Start with a verb: "Add", "Fix", "Remove", "Change", "Update"
+   - Be specific: "Fix crash when input file is empty" not "Fix bug"
+   - Delete sections that don't apply to your PR
+
+3. EXAMPLES
+
+   Good:
+   - Add `--threads` flag for parallel sequence alignment
+   - Fix memory leak when processing large FASTA files
+   - Change `--output` to `--output-dir` for clarity
+
+   Bad:
+   - Added new feature
+   - Fixed bug
+   - Updated code
+
+-->
diff --git a/.github/RELEASE_TEMPLATE.md b/.github/RELEASE_TEMPLATE.md
new file mode 100644
index 0000000..0ca0409
--- /dev/null
+++ b/.github/RELEASE_TEMPLATE.md
@@ -0,0 +1,41 @@
+## What's New
+
+${SUMMARY}
+
+## Features
+
+${FEATURES}
+
+## Bug Fixes
+
+${BUG_FIXES}
+
+## Breaking Changes
+
+${BREAKING_CHANGES}
+
+## Installation
+
+Download the appropriate archive for your system:
+- `seq_sim-${VERSION}.tar` - Unix/Linux/macOS
+- `seq_sim-${VERSION}.zip` - Windows
+
+### Quick Start
+
+```bash
+# Extract the archive
+tar -xf seq_sim-${VERSION}.tar
+# or
+unzip seq_sim-${VERSION}.zip
+
+# Run the application
+./seq_sim-${VERSION}/bin/seq_sim --help
+```
+
+## Requirements
+
+- Java 21 or higher
+
+## Full Changelog
+
+**Full Changelog**: https://github.com/${REPO}/compare/${PREVIOUS_TAG}...${VERSION}
diff --git a/.github/workflows/pr-check.yml b/.github/workflows/pr-check.yml
new file mode 100644
index 0000000..269773d
--- /dev/null
+++ b/.github/workflows/pr-check.yml
@@ -0,0 +1,71 @@
+name: PR Version Check
+
+on:
+  pull_request:
+    branches:
+      - main
+      - master
+
+jobs:
+  version-check:
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get version from build.gradle.kts
+        id: get_version
+        run: |
+          VERSION=$(grep -oP 'version\s*=\s*"\K[^"]+' build.gradle.kts)
+          echo "version=v$VERSION" >> $GITHUB_OUTPUT
+          echo "PR version: v$VERSION"
+
+      - name: Get current latest tag
+        id: get_current_tag
+        run: |
+          CURRENT_TAG=$(git describe --tags --abbrev=0 origin/main 2>/dev/null || git describe --tags --abbrev=0 origin/master 2>/dev/null || echo "v0.0.0")
+          echo "current_tag=$CURRENT_TAG" >> $GITHUB_OUTPUT
+          echo "Current released version: $CURRENT_TAG"
+
+      - name: Validate version is higher than current release
+        run: |
+          CURRENT="${{ steps.get_current_tag.outputs.current_tag }}"
+          NEW="${{ steps.get_version.outputs.version }}"
+          
+          # Function to convert version to comparable number
+          version_to_num() {
+            local version=$1
+            # Remove 'v' prefix if present
+            version=${version#v}
+            # Split into parts and pad (handles 2 or 3 part versions)
+            echo "$version" | awk -F. '{ printf "%d%03d%03d", $1, ($2 ? $2 : 0), ($3 ? $3 : 0) }'
+          }
+          
+          CURRENT_NUM=$(version_to_num "$CURRENT")
+          NEW_NUM=$(version_to_num "$NEW")
+          
+          echo "Comparing versions:"
+          echo "  Current release: $CURRENT ($CURRENT_NUM)"
+          echo "  PR version:      $NEW ($NEW_NUM)"
+          
+          if [ "$NEW_NUM" -le "$CURRENT_NUM" ]; then
+            echo ""
+            echo "::error::Version must be updated before merging!"
+            echo "::error::Current released version is $CURRENT"
+            echo "::error::Please update the 'version' in build.gradle.kts to be higher than $CURRENT"
+            echo ""
+            echo "To fix this, update build.gradle.kts:"
+            echo '  version = "X.Y.Z"  // Must be higher than current'
+            echo ""
+            echo "Version guidelines (semantic versioning):"
+            echo "  - MAJOR (X): Breaking changes"
+            echo "  - MINOR (Y): New features (backwards compatible)"
+            echo "  - PATCH (Z): Bug fixes"
+            exit 1
+          fi
+          
+          echo ""
+          echo "Version check passed: $NEW > $CURRENT"
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 0000000..6a7d9f9
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,211 @@
+name: Build and Release
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get version from build.gradle.kts
+        id: get_version
+        run: |
+          VERSION=$(grep -oP 'version\s*=\s*"\K[^"]+' build.gradle.kts)
+          echo "version=v$VERSION" >> $GITHUB_OUTPUT
+          echo "Extracted version: v$VERSION"
+
+      - name: Get current latest tag
+        id: get_current_tag
+        run: |
+          CURRENT_TAG=$(git describe --tags --abbrev=0 2>/dev/null || echo "v0.0.0")
+          echo "current_tag=$CURRENT_TAG" >> $GITHUB_OUTPUT
+          echo "Current latest tag: $CURRENT_TAG"
+
+      - name: Check if version already released
+        id: check_version
+        run: |
+          VERSION="${{ steps.get_version.outputs.version }}"
+          CURRENT="${{ steps.get_current_tag.outputs.current_tag }}"
+          
+          # Check if this version tag already exists
+          if git rev-parse "$VERSION" >/dev/null 2>&1; then
+            echo "Version $VERSION already released, skipping"
+            echo "skip_release=true" >> $GITHUB_OUTPUT
+            exit 0
+          fi
+          
+          echo "skip_release=false" >> $GITHUB_OUTPUT
+          echo "New version $VERSION will be released"
+
+      - name: Set up JDK 21
+        if: steps.check_version.outputs.skip_release != 'true'
+        uses: actions/setup-java@v4
+        with:
+          java-version: '21'
+          distribution: 'temurin'
+
+      - name: Setup Gradle
+        if: steps.check_version.outputs.skip_release != 'true'
+        uses: gradle/actions/setup-gradle@v4
+
+      - name: Grant execute permission for gradlew
+        if: steps.check_version.outputs.skip_release != 'true'
+        run: chmod +x gradlew
+
+      - name: Build distributions
+        if: steps.check_version.outputs.skip_release != 'true'
+        run: ./gradlew distTar distZip
+
+      - name: Extract release notes from merged PRs
+        id: extract_pr_notes
+        if: steps.check_version.outputs.skip_release != 'true'
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          PREVIOUS_TAG="${{ steps.get_current_tag.outputs.current_tag }}"
+          
+          # Get the date of the previous tag, or use epoch if no previous tag
+          if [ -n "$PREVIOUS_TAG" ] && [ "$PREVIOUS_TAG" != "v0.0.0" ]; then
+            SINCE_DATE=$(git log -1 --format=%aI "$PREVIOUS_TAG")
+          else
+            SINCE_DATE="1970-01-01T00:00:00Z"
+          fi
+          
+          # Fetch merged PRs since the previous tag
+          PR_BODIES=$(gh pr list --state merged --search "merged:>=$SINCE_DATE" --json body --jq '.[].body // ""')
+          
+          # Initialize section collectors
+          FEATURES=""
+          BUG_FIXES=""
+          BREAKING_CHANGES=""
+          SUMMARIES=""
+          
+          # Function to extract section content from PR body
+          extract_section() {
+            local body="$1"
+            local section="$2"
+            echo "$body" | awk -v section="$section" '
+              BEGIN { in_section=0 }
+              /^## / { 
+                if ($0 ~ "^## " section) { in_section=1; next }
+                else { in_section=0 }
+              }
+              /^---/ { in_section=0 }
+              in_section && /^- .+/ { print }
+            '
+          }
+          
+          # Process each PR body
+          while IFS= read -r body; do
+            [ -z "$body" ] && continue
+            
+            # Extract Summary (single paragraph after ## Summary)
+            summary=$(echo "$body" | awk '
+              BEGIN { in_section=0 }
+              /^## Summary/ { in_section=1; next }
+              /^## / { in_section=0 }
+              /^---/ { in_section=0 }
+              in_section && /^[^<]/ && !/^$/ { print; exit }
+            ')
+            [ -n "$summary" ] && SUMMARIES="${SUMMARIES}${summary}"$'\n'
+            
+            # Extract Features
+            features=$(extract_section "$body" "Features")
+            [ -n "$features" ] && FEATURES="${FEATURES}${features}"$'\n'
+            
+            # Extract Bug Fixes
+            bugfixes=$(extract_section "$body" "Bug Fixes")
+            [ -n "$bugfixes" ] && BUG_FIXES="${BUG_FIXES}${bugfixes}"$'\n'
+            
+            # Extract Breaking Changes
+            breaking=$(extract_section "$body" "Breaking Changes")
+            [ -n "$breaking" ] && BREAKING_CHANGES="${BREAKING_CHANGES}${breaking}"$'\n'
+            
+          done <<< "$PR_BODIES"
+          
+          # Set defaults if empty
+          [ -z "$SUMMARIES" ] && SUMMARIES="See individual changes below."
+          [ -z "$FEATURES" ] && FEATURES="- None"
+          [ -z "$BUG_FIXES" ] && BUG_FIXES="- None"
+          [ -z "$BREAKING_CHANGES" ] && BREAKING_CHANGES="- None"
+          
+          # Write to temp files (handles multiline content)
+          echo "$SUMMARIES" > /tmp/summaries.txt
+          echo "$FEATURES" > /tmp/features.txt
+          echo "$BUG_FIXES" > /tmp/bugfixes.txt
+          echo "$BREAKING_CHANGES" > /tmp/breaking.txt
+
+      - name: Generate release notes from template
+        if: steps.check_version.outputs.skip_release != 'true'
+        run: |
+          VERSION="${{ steps.get_version.outputs.version }}"
+          PREVIOUS_TAG="${{ steps.get_current_tag.outputs.current_tag }}"
+          REPO="${{ github.repository }}"
+          
+          # Read extracted PR content
+          SUMMARY=$(cat /tmp/summaries.txt)
+          FEATURES=$(cat /tmp/features.txt)
+          BUG_FIXES=$(cat /tmp/bugfixes.txt)
+          BREAKING_CHANGES=$(cat /tmp/breaking.txt)
+          
+          # Read template
+          NOTES=$(cat .github/RELEASE_TEMPLATE.md)
+          
+          # Substitute variables using sed for multiline content
+          echo "$NOTES" | \
+            sed "s|\${VERSION}|$VERSION|g" | \
+            sed "s|\${REPO}|$REPO|g" | \
+            sed "s|\${PREVIOUS_TAG}|$PREVIOUS_TAG|g" > release_notes.md
+          
+          # Replace section placeholders with content
+          sed -i "s|\${SUMMARY}|$SUMMARY|g" release_notes.md
+          
+          # Use awk for multiline replacements
+          awk -v features="$FEATURES" '{gsub(/\${FEATURES}/, features)}1' release_notes.md > tmp && mv tmp release_notes.md
+          awk -v bugfixes="$BUG_FIXES" '{gsub(/\${BUG_FIXES}/, bugfixes)}1' release_notes.md > tmp && mv tmp release_notes.md
+          awk -v breaking="$BREAKING_CHANGES" '{gsub(/\${BREAKING_CHANGES}/, breaking)}1' release_notes.md > tmp && mv tmp release_notes.md
+
+      - name: Create version tag
+        if: steps.check_version.outputs.skip_release != 'true'
+        run: |
+          VERSION="${{ steps.get_version.outputs.version }}"
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git tag -a "$VERSION" -m "Release $VERSION"
+          git push origin "$VERSION"
+          echo "Created and pushed tag: $VERSION"
+
+      - name: Upload distribution artifacts
+        if: steps.check_version.outputs.skip_release != 'true'
+        uses: actions/upload-artifact@v4
+        with:
+          name: distributions
+          path: |
+            build/distributions/*.tar
+            build/distributions/*.zip
+
+      - name: Create Release
+        if: steps.check_version.outputs.skip_release != 'true'
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: ${{ steps.get_version.outputs.version }}
+          name: Release ${{ steps.get_version.outputs.version }}
+          draft: false
+          prerelease: false
+          files: |
+            build/distributions/*.tar
+            build/distributions/*.zip
+          body_path: release_notes.md