Editing multiple sequence alignments (MSAs) in Jalview allows you to manually correct alignment errors, adjust gaps, and manage your sequences. It provides two primary modes for manual refinement: Normal Mode (mouse-driven) and Cursor Mode (keyboard-driven).
💡 Pro-Tip before you begin: For large alignments, go to the top menu and uncheck Calculate → Autocalculate Consensus. This stops Jalview from recalculating conservation scores after every single gap you move, preventing severe lag. 🖱️ Normal Mode (Using the Mouse)
Normal Mode is the default setting in Jalview. You modify alignments by clicking and dragging residues or gaps.
Edit a single sequence: Hold Shift, click on a residue or gap, and drag left or right to delete or insert gaps.
Edit multiple sequences (Group Edit): Highlight a group of sequences or columns first. Hold Ctrl (Cmd on Mac), click a residue within the selection, and drag it to insert or remove gaps across the entire group simultaneously.
Locked Editing: Select a block of columns (e.g., columns 45 to 55). Hold Shift and drag a residue inside that selection. The edits will shift the residues, but the movement will be strictly bound within the boundaries of your selected columns. ⌨️ Cursor Mode (Using the Keyboard)
If you prefer precise, keystroke-based modifications, you can toggle into Cursor Mode.
Press F2 to enter Cursor Mode (a visible keyboard cursor will appear on your grid).
Use your standard arrow keys to navigate around the alignment grid. Press Spacebar to insert a gap at the cursor position. Press Backspace or Delete to remove a gap. Press F2 again to exit and return to Normal Mode. 📂 Reordering, Hiding, and Deleting Sequences
You can quickly organize the structural layout of your alignment window through the sequence ID panel on the left.
Reorder Sequences: Click a sequence name in the ID panel. Use the Up Arrow or Down Arrow keys to physically shift its vertical position in the alignment window.
Hide Regions/Sequences: Select the sequence IDs or columns you want to temporarily remove from view, right-click, and select Hide Sequences (or Hide Columns). A small blue triangle will appear where they are masked; right-clicking this triangle lets you Reveal them.
Mass Removal: If you need to wipe out all gaps entirely to restart a clean alignment web service, navigate to the top edit menu to clear out the blank characters or use standard Ctrl + X / Delete keys on highlighted blocks. 🧪 Editing Sequence Regions Manually
If you need to edit an exact sequence block or manually patch a specific string of amino acids/nucleotides: Right-click on a sequence row. Navigate to Sequence → Edit → Edit Sequence.
This opens a text dialog window allowing you to type, overwrite, or delete characters directly within that specific sequence.
To learn more about advanced alignment strategies, check out the official Jalview Editing Tutorial or browse their comprehensive Video Demonstration Guides. To help tailor this, let me know:
Are you working with protein or nucleotide (DNA/RNA) sequences?
Do you need to run an automated alignment tool (like Clustal Omega or MAFFT) directly inside Jalview first?
Are you trying to fix a specific alignment error (like mismatched structural loops)? Editing Alignments – Jalview
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