Alignment Viewer

A quick and simple FASTA alignment viewer for Python notebooks with colored sequence visualization.

Features

• Color-coded nucleotide display
• Support for both Jupyter notebooks and terminal output
• Configurable display options (number of sequences, columns, ruler, etc.)
• Scrollable alignment view in notebooks
• Block-based sequence formatting

Installation

pip install git+https://github.com/ECV-Lab-KULeuven/AlignmentViewer.git

Usage

from AlignmentViewer import AlignmentViewer

# Display alignment from file
AlignmentViewer.display_alignment("data/alignment.fasta", nseqs=5, ncols=50)

Configuration

You can customize the display using the following parameters:

• nseqs: Number of sequences to display (default: 10)
• ncols: Number of columns to display (default: 100)
• show_ruler: Show position ruler (default: True)
• block_size: Size of sequence blocks (default: 10)
• start_pos: Starting position for display (default: 0)
• container_height: Height of the scrollable container in notebooks (default: "300px")
• as_html: Return HTML string instead of displaying in notebook (default: check)

License

MIT License