Performs multiple sequence alignment using MAFFT (if needed) and visualizes the resulting alignment using pyMSAviz. The visualization automatically adapts its layout to long alignments by splitting them into multiple pages (PNG files).

Features:

• Automatic MAFFT alignment (if sequences not pre-aligned)
• Auto-detection of nucleotide vs protein color scheme
• Pagination for long alignments Output:
• .aln.fa : aligned FASTA file
• .page_*.png : paginated alignment images