Qwen MSA Viewer

MSA Viewer - Keyboard Shortcuts

                Ctrl+LLoad file
                Ctrl+ASelect/deselect all
                Ctrl+CCopy sequence name
                Ctrl+Shift+CCopy selected sequences
                Ctrl+DelDelete selected
                Ctrl+ZUndo
                Ctrl+YRedo
                Ctrl+RReverse complement
                Ctrl+UDuplicate
                Ctrl+BConsensus below
                Ctrl+UpMove selected up
                Ctrl+DownMove selected down
                Ctrl+HomeMove to top
                Ctrl+EndMove to bottom
                Ctrl+Shift+VCopy columns
                Ctrl+Shift+DDelete columns
                Ctrl+Shift+RRealign block
                Ctrl+TOpen in new tab
                Ctrl+SSave preset
                Ctrl+OLoad preset
                Ctrl+HHide/show menu
                Ctrl+IShow this info
            

Sequence Editor

Name:

Edit the sequence text below (standard text editing: select, delete, type, Ctrl+C/V/X). Length: 0

Pad/trim to alignment length

Add Sequences

Paste new sequences in FASTA format. "Just Add" appends them (padded with gaps). "Add & Align" realigns everything with MAFFT (runs locally via WebAssembly).

Place at top Align to consensus

Dot Plot

Window: Threshold: 55% RevComp B

A: —
   
B: —

Repeat & TSD Finder

Analysis: Tandem repeats Direct repeats Inverted repeats TSD finder

Min length: Max divergence: %

                Click "Run Analysis" to start.
            

MSA Viewer - Keyboard Shortcuts

Color Assignment History

Sequence Clustering Results

Sequence Editor

Add Sequences

Dot Plot

Repeat & TSD Finder