chore: Convert American spellings to British English

.github/ISSUE_TEMPLATE/bug_report.md

@@ -16,11 +16,11 @@ A clear and concise description of what the bug is.
 2. Run command '...'
 3. See error
 
-## ✅ Expected Behavior
+## ✅ Expected Behaviour
 
 A clear and concise description of what you expected to happen.
 
-## ❌ Actual Behavior
+## ❌ Actual Behaviour
 
 What actually happened instead.
 

.github/codeql/codeql-config.yml

@@ -10,7 +10,7 @@ on:
 
 jobs:
   # CodeQL analysis for supported languages
-  analyze:
+  analyse:
     name: CodeQL Analyze (${{ matrix.language }})
     runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
     permissions:
@@ -35,7 +35,7 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Initialize CodeQL
+      - name: Initialise CodeQL
         uses: github/codeql-action/init@v3
         with:
           # matrix.language is one of the languages above
@@ -53,4 +53,4 @@ jobs:
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@v3
         with:
-          category: "/language:${{matrix.language}}"
+          category: "/language:${{matrix.language}}"

.github/workflows/codeql-analysis.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v6
 
-      - name: Initialize CodeQL using repo config
+      - name: Initialise CodeQL using repo config
         uses: github/codeql-action/init@v4
         with:
           config-file: .github/codeql/codeql-config.yml

CODE_OF_CONDUCT.md

@@ -14,7 +14,7 @@ diverse, inclusive, and healthy community.
 
 ## Our Standards
 
-Examples of behavior that contributes to a positive environment for our
+Examples of behaviour that contributes to a positive environment for our
 community include:
 
 * Demonstrating empathy and kindness toward other people
@@ -25,7 +25,7 @@ community include:
 * Focusing on what is best not just for us as individuals, but for the
   overall community
 
-Examples of unacceptable behavior include:
+Examples of unacceptable behaviour include:
 
 * The use of sexualised language or imagery, and sexual attention or
   advances of any kind
@@ -39,8 +39,8 @@ Examples of unacceptable behavior include:
 ## Enforcement Responsibilities
 
 Community leaders are responsible for clarifying and enforcing our standards of
-acceptable behavior and will take appropriate and fair corrective action in
-response to any behavior that they deem inappropriate, threatening, offensive,
+acceptable behaviour and will take appropriate and fair corrective action in
+response to any behaviour that they deem inappropriate, threatening, offensive,
 or harmful.
 
 Community leaders have the right and responsibility to remove, edit, or reject
@@ -58,7 +58,7 @@ representative at an online or offline event.
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be
+Instances of abusive, harassing, or otherwise unacceptable behaviour may be
 reported to the community leaders responsible for enforcement at
 .
 All complaints will be reviewed and investigated promptly and fairly.
@@ -73,12 +73,12 @@ the consequences for any action they deem in violation of this Code of Conduct:
 
 ### 1. Correction
 
-**Community Impact**: Use of inappropriate language or other behavior deemed
+**Community Impact**: Use of inappropriate language or other behaviour deemed
 unprofessional or unwelcome in the community.
 
 **Consequence**: A private, written warning from community leaders, providing
 clarity around the nature of the violation and an explanation of why the
-behavior was inappropriate. A public apology may be requested.
+behaviour was inappropriate. A public apology may be requested.
 
 ### 2. Warning
 
@@ -106,7 +106,7 @@ Violating these terms may lead to a permanent ban.
 ### 4. Permanent Ban
 
 **Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior,  harassment of an
+standards, including sustained inappropriate behaviour,  harassment of an
 individual, or aggression toward or disparagement of classes of individuals.
 
 **Consequence**: A permanent ban from any sort of public interaction within

README.md

@@ -82,7 +82,7 @@ Rscript -e "install.packages('BiocManager'); BiocManager::install('dada2')"
 ### View Results
 
 ```bash
-# Interactive taxonomy visualization
+# Interactive taxonomy visualisation
 open results/06-viz/taxa_krona.html
 
 # ASV abundance table
@@ -106,9 +106,9 @@ FASTQ Input
 [03] Chimera QC    → VSEARCH UCHIME hybrid detection (GPU-optional)
 [04] Taxonomy      → RDP Classifier (Bayesian)
 [05] Phylogenetics → FastTree 2 (ML tree, GPU-optional)
-[06] Visualization → Krona interactive charts
+[06] Visualisation → Krona interactive charts
     ↓
-Publication-Ready Tables + Interactive Visualization
+Publication-Ready Tables + Interactive Visualisation
 ```
 
 **Performance:** 
@@ -132,7 +132,7 @@ NucleiTaxa/
 │   ├── 03-chimera-vsearch.sh   # Hybrid chimera detection
 │   ├── 04-taxonomy-rdp.sh      # Taxonomy assignment
 │   ├── 05-phylo-fasttree.sh    # Phylogenetic tree
-│   └── 06-krona-viz.sh         # Interactive visualization
+│   └── 06-krona-viz.sh         # Interactive visualisation
 ├── analytics/
 │   ├── server/
 │   │   └── nucleitaxa-server.cpp  # C++ WebSocket backend
@@ -417,7 +417,7 @@ If you use NucleiTaxa in your research, please cite:
 
 ---
 
-## 📄 License
+## 📄 Licence
 
 GNU General Public License v3.0 (GPL-3.0) - See [LICENSE](LICENSE) file
 

SECURITY.md

@@ -40,7 +40,7 @@ This security policy applies to:
 - Official releases
 - Documentation
 
-## Acknowledgments
+## Acknowledgements
 
 We appreciate responsible disclosure and will acknowledge security researchers who report valid vulnerabilities.
 

docs/CUDA_ACCELERATION.md

@@ -10,7 +10,7 @@
 Do you have NVIDIA GPU?
     ├─ Yes, CUDA-capable (compute capability 3.0+)
     │   ├─ Consumer GPU (GTX 1080, RTX 2080, etc.) → 10-50x speedup
-    │   ├─ Data center (A100, H100) → 50-200x speedup
+    │   ├─ Data centre (A100, H100) → 50-200x speedup
     │   └─ Follow setup below
     │
     └─ No → Use CPU-only (default, fully supported)
@@ -140,7 +140,7 @@ vsearch --usearch_global test.fasta --db ref.fasta --id 0.85 --cuda
 
 ### Phase 3: FastTree GPU (Promising)
 - **Status:** FastTree 2.1.0+ supports GPU via OpenCL (partial)
-- **Alternative:** Use VeryFastTree (GPU-optimized phylogenetic inference)
+- **Alternative:** Use VeryFastTree (GPU-optimised phylogenetic inference)
   ```bash
   # Instead of FastTree 2
   veryfasttree -nt -fastest -input input.fasta -output tree.nwk
@@ -149,9 +149,9 @@ vsearch --usearch_global test.fasta --db ref.fasta --id 0.85 --cuda
 - **Implementation:** Add `--gpu-phylo` flag
 - **Timeline:** Q2 2026
 
-### Phase 4: WebGL Visualization (Client-side)
+### Phase 4: WebGL Visualisation (Client-side)
 - **Status:** D3.js + Three.js can leverage WebGL for GPU rendering
-- **Optimization:** Ren 1M+ points on interactive charts
+- **Optimisation:** Ren 1M+ points on interactive charts
 - **Tools:** Pixi.js, Babylon.js for WebGL acceleration
 - **Timeline:** Q3 2026
 
@@ -191,7 +191,7 @@ vsearch --usearch_global test.fasta --db ref.fasta --id 0.85 --cuda
 watch -n 0.5 nvidia-smi
 
 # During pipeline run, you should see:
-# nvidia-smi output showing utilization %
+# nvidia-smi output showing utilisation %
 ```
 
 ---
@@ -281,7 +281,7 @@ QIIME2 doesn't natively support GPU, but you can:
 
 1. Run NucleiTaxa with `--cuda` to get faster denoising/taxonomy
 2. Export results to QIIME2 format (already supported)
-3. Continue analysis in QIIME2 with CPU (GPU gains already realized)
+3. Continue analysis in QIIME2 with CPU (GPU gains already realised)
 
 ```bash
 # Fast GPU denoising + chimera removal
@@ -299,7 +299,7 @@ qiime tools import \
 
 **2025 Research:**
 - VSEARCH GPU: Edgar et al. (2023) - CUDA implementation in mainline
-- VeryFastTree: GPU-optimized phylogenetic inference (published 2024)
+- VeryFastTree: GPU-optimised phylogenetic inference (published 2024)
 - NVIDIA cuVS: 125x speedup for vector search (2025)
 
 **Tools:**
@@ -346,7 +346,7 @@ GPU acceleration is an active research area! Contributions welcome:
 
 - [ ] Implement DADA2 GPU kernels (CUDA/HIP)
 - [ ] Add VeryFastTree integration
-- [ ] Optimize WebGL rendering for 10M+ points
+- [ ] Optimise WebGL rendering for 10M+ points
 - [ ] Test on AMD GPUs (ROCm)
 - [ ] Performance profiling + benchmarks
 
@@ -358,7 +358,7 @@ GPU acceleration is an active research area! Contributions welcome:
 - ✅ VSEARCH GPU (done, native support)
 - 🔄 DADA2 GPU (research, experimental)
 - 🔄 VeryFastTree integration (ready to integrate)
-- 📊 WebGL-accelerated visualization (frontend optimization)
+- 📊 WebGL-accelerated visualisation (frontend optimisation)
 - 🔬 End-to-end GPU pipeline for 100M+ read datasets
 
 This is the bleeding-edge bioinformatics computing we're building! 🚀

docs/PHASE_1_IMPLEMENTATION.md

@@ -15,7 +15,7 @@
 - ✅ Added `--cuda-stages` for selective GPU acceleration (e.g., `--cuda-stages "03,05"`)
 - ✅ Auto-detection: Runs `nvidia-smi` to verify GPU availability, gracefully falls back to CPU
 - ✅ Enhanced logging with GPU status and execution times
-- ✅ Stage-by-stage execution with color-coded output
+- ✅ Stage-by-stage execution with colour-coded output
 
 **Usage Examples:**
 ```bash
@@ -95,7 +95,7 @@ cat test_benchmarks/results.csv
 | GPU Class | Expected Speedup | Notes |
 |-----------|------------------|-------|
 | RTX 2080  | 8-10x | Consumer GPU, good cost/performance |
-| A100      | 12-15x | Enterprise GPU, memory-optimized |
+| A100      | 12-15x | Enterprise GPU, memory-optimised |
 | H100      | 15-20x | Latest NVIDIA, peak performance |
 | **No GPU (CPU)** | **1.0x** | Baseline (4-6 threads) |
 
@@ -151,7 +151,7 @@ cat test_benchmarks/results.csv
 
 1. **bin/nucleitaxa** (+85 lines)
    - GPU detection and flag routing
-   - Enhanced logging with color codes
+   - Enhanced logging with colour codes
    - Resume capability for failed runs
 
 2. **pipeline/03-chimera-vsearch.sh** (+200 lines)
@@ -194,7 +194,7 @@ be07f7b [Main] Initial commit from cuda-expansion PR
 - Status: Requires R/CUDA expertise, potential academic collaboration
 - Alternative: Investigate cuDASH (if available)
 
-### Phase 4: WebGL GPU Acceleration for Visualization (2-4 weeks)
+### Phase 4: WebGL GPU Acceleration for Visualisation (2-4 weeks)
 - D3.js + Three.js WebGL rendering
 - GPU-accelerated taxonomy tree rendering
 - Support for 1M+ sequences in interactive view

pipeline/05-phylo-fasttree.sh

@@ -4,7 +4,7 @@
 # NucleiTaxa Pipeline Stage 05: Phylogenetic Tree Construction
 # 
 # FastTree 2 (ultra-fast maximum-likelihood tree inference)
-# - 1000x faster than UPGMA or neighbor-joining
+# - 1000x faster than UPGMA or neighbour-joining
 # - Better accuracy for large alignments (10K+ sequences)
 # - Suitable for microbiome ASV trees
 #
@@ -141,7 +141,7 @@ log_info "=== Building Maximum-Likelihood Tree ==="
 # -gtr:          Use GTR model (more accurate than JC69)
 # -gamma:        Model gamma distribution of rates (accounting for site-to-site variation)
 # -quiet:        Minimal output
-# Additional performance: -mlnni 4 (ML nearest neighbor interchanges)
+# Additional performance: -mlnni 4 (ML nearest neighbour interchanges)
 
 FASTTREE_OPTS="-nt -gtr -gamma -quiet"
 
@@ -304,7 +304,7 @@ OUTPUTS:
   - phylo_metrics.txt (phylogenetic diversity)
 
 NEXT STAGE:
-  Proceed to 06-krona-viz.sh for interactive taxonomy visualization
+  Proceed to 06-krona-viz.sh for interactive taxonomy visualisation
 
 INTERPRETATION:
   Tree branch lengths represent evolutionary distance