Update README.md

highlight commands

Author: Karo555

README.md

@@ -2,13 +2,13 @@
 bIOINFORMATICS @WUST
 
 # Installation
-git clone https://github.com/Karo555/needleman-wunsch.git <br>
-cd needleman-wunsch-aligner <br>
-pip install -e .[html,pdf]
+`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) <br>
-needleman-wunsch --manual
+`needleman-wunsch --manual`
 
 You’ll be prompted to enter:
 - Sequence 1 ID
@@ -17,26 +17,26 @@ You’ll be prompted to enter:
 - Sequence 2
 
 2. FASTA file input <br>
-needleman-wunsch --input data/seq1.fasta data/seq2.fasta --output reports/alignment.txt <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. <br>
 The text report is saved to reports/alignment.txt <br>
 
 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
+`needleman-wunsch --input data/seq1.fasta data/seq2.fasta --match 2 --mismatch -1 --gap -2`
 
 4. Enumerate all optimal alignments <br>
-needleman-wunsch --input data/seq1.fasta data/seq2.fasta --all-paths --output reports/all_paths.txt
+`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 <br>
-needleman-wunsch --input data/seq1.fasta data/seq2.fasta --matrix-out reports/matrix.csv
+`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 <br>
-needleman-wunsch --input data/seq1.fasta data/seq2.fasta --json reports/alignment.json
+`needleman-wunsch --input data/seq1.fasta data/seq2.fasta --json reports/alignment.json`
 
 Produces a JSON file containing: <br>
 
@@ -46,12 +46,12 @@ Full DP matrix
 All alignments with per-path statistics
 
 7. Heatmap visualization <br>
-needleman-wunsch --input data/seq1.fasta data/seq2.fasta --plot plots/heatmap.png
+`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 <br>
-needleman-wunsch --input data/seq1.fasta data/seq2.fasta --plot plots/heatmap.png --html reports/alignment.html
+`needleman-wunsch --input data/seq1.fasta data/seq2.fasta --plot plots/heatmap.png --html reports/alignment.html`
 
 Generates a standalone HTML page embedding:
 
@@ -61,15 +61,15 @@ Inline statistics
 The heatmap image (correctly linked)
 
 Open it in your browser via:
-python3 -m http.server 8000
+`python -m http.server 8000`
 
-then visit http://localhost:8000/reports/alignment.html
+then visit `http://localhost:8000/reports/alignment.html`
 
 9. PDF summary report <br>
-needleman-wunsch --input data/seq1.fasta data/seq2.fasta --plot plots/heatmap.png --pdf reports/alignment.pdf
+`needleman-wunsch --input data/seq1.fasta data/seq2.fasta --plot plots/heatmap.png --pdf reports/alignment.pdf`
 
 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
+`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)<br>
 reports/matrix.csv (raw DP matrix)<br>