Update README.md

Author: Karo555

README.md

@@ -2,12 +2,12 @@
 bIOINFORMATICS @WUST
 
 # Installation
-git clone https://github.com/Karo555/needleman-wunsch.git
-cd needleman-wunsch-aligner
+git clone https://github.com/Karo555/needleman-wunsch.git <br>
+cd needleman-wunsch-aligner <br>
 pip install -e .[html,pdf]
 
 # Usage
-1. Basic DNA alignment (manual input)
+1. Basic DNA alignment (manual input) <br>
 needleman-wunsch --manual
 
 You’ll be prompted to enter:
@@ -16,41 +16,41 @@ You’ll be prompted to enter:
 - Sequence 1
 - Sequence 2
 
-2. FASTA file input
-needleman-wunsch --input data/seq1.fasta data/seq2.fasta --output reports/alignment.txt
+2. FASTA file input <br>
+needleman-wunsch --input data/seq1.fasta data/seq2.fasta --output reports/alignment.txt <br>
 
-data/seq1.fasta and data/seq2.fasta each contain exactly one record.
-The text report is saved to reports/alignment.txt
+data/seq1.fasta and data/seq2.fasta each contain exactly one record. <br>
+The text report is saved to reports/alignment.txt <br>
 
-3. Custom scoring: override match, mismatch, and gap scores
+3. Custom scoring. Override match, mismatch, and gap scores. <br>
 needleman-wunsch --input data/seq1.fasta data/seq2.fasta --match 2 --mismatch -1 --gap -2
 
-4. Enumerate all optimal alignments
+4. Enumerate all optimal alignments <br>
 needleman-wunsch --input data/seq1.fasta data/seq2.fasta --all-paths --output reports/all_paths.txt
 
 Lists every equally optimal alignment and writes them to reports/all_paths.txt.
 
-5. Export raw DP matrix as CSV
+5. Export raw DP matrix as CSV <br>
 needleman-wunsch --input data/seq1.fasta data/seq2.fasta --matrix-out reports/matrix.csv
 
 The full (N+1)×(M+1) score matrix is saved in comma‐separated format for downstream analysis
 
-6. Structured JSON output
+6. Structured JSON output <br>
 needleman-wunsch --input data/seq1.fasta data/seq2.fasta --json reports/alignment.json
 
-Produces a JSON file containing:
+Produces a JSON file containing: <br>
 
 Original sequences and IDs
 Scoring parameters
 Full DP matrix
 All alignments with per-path statistics
 
-7. Heatmap visualization
+7. Heatmap visualization <br>
 needleman-wunsch --input data/seq1.fasta data/seq2.fasta --plot plots/heatmap.png
 
 Renders the DP matrix as a heatmap PNG saved to plots/heatmap.png.
 
-8. HTML summary report
+8. HTML summary report <br>
 needleman-wunsch --input data/seq1.fasta data/seq2.fasta --plot plots/heatmap.png --html reports/alignment.html
 
 Generates a standalone HTML page embedding:
@@ -65,19 +65,19 @@ python3 -m http.server 8000
 
 then visit http://localhost:8000/reports/alignment.html
 
-9. PDF summary report
+9. PDF summary report <br>
 needleman-wunsch --input data/seq1.fasta data/seq2.fasta --plot plots/heatmap.png --pdf reports/alignment.pdf
 
-10. one shot
+10. one shot <br>
 needleman-wunsch --input data/seq1.fasta data/seq2.fasta --all-paths --match 2 --mismatch -1 --gap -2 --output reports/alignment.txt --matrix-out reports/matrix.csv --json reports/alignment.json --plot plots/heatmap.png --html reports/alignment.html --pdf reports/alignment.pdf
 
-reports/alignment.txt (text report)
-reports/matrix.csv (raw DP matrix)
-reports/alignment.json (structured JSON)
-plots/heatmap.png (heatmap image)
-reports/alignment.html (HTML summary)
-reports/alignment.pdf (PDF summary)
+reports/alignment.txt (text report)<br>
+reports/matrix.csv (raw DP matrix)<br>
+reports/alignment.json (structured JSON)<br>
+plots/heatmap.png (heatmap image)<br>
+reports/alignment.html (HTML summary)<br>
+reports/alignment.pdf (PDF summary)<br>
 
 
-## 📄 License
-This project is licensed under the MIT License. See [LICENSE](LICENSE) for details.
+## 📄 License<br>
+This project is licensed under the MIT License. See [LICENSE](LICENSE) for details.<br>