MSA Viewer
The MSA viewer appears when the dataset includes alignment data. It can be opened from the sidebar Sequence Alignment section or from the timeline shortcut.
Sidebar Controls
| Control | Meaning |
|---|---|
| Open Alignment | Opens the floating alignment viewer. |
| Follow Current Window | Keeps the viewer synchronized with the current input tree or timeline segment. |
If Follow Current Window is disabled, the MSA viewer keeps its current viewport while the tree movie moves.
When Follow Current Window is enabled, synchronization follows the current input-tree/window index. During an interpolated transition, the tree viewer distinguishes the source tree and target tree; the MSA viewer follows the corresponding input window rather than redrawing for every intermediate interpolation frame.
Active Region
| Control | Meaning |
|---|---|
| Region | Displays the alignment-column range associated with the active movie window. |
The region is read-only. When Follow Current Window is enabled, it follows the active movie window.
View Actions
| Control | Meaning |
|---|---|
| Zoom in alignment | Increases alignment zoom. |
| Zoom out alignment | Decreases alignment zoom. |
| Reset alignment view | Restores the default alignment viewport. |
The viewer also has horizontal and vertical scrollbars for navigating long alignments and many taxa.
Row Order
| Control | Meaning |
|---|---|
| Match Tree Order | Reorders alignment rows to match the visible tree leaf order. |
| Reset Order | Restores the default alignment row order. |
Matching tree order helps compare moving clades with their sequence rows.
Coloring
The alignment viewer supports these color schemes:
| Scheme | Use |
|---|---|
| None (Empty) | Removes residue background coloring. |
| Default | General residue coloring. |
| Clustal / Clustal2 | Clustal-style residue classes. |
| Hydrophobicity, Zappo, Taylor, Buried, Cinema, Helix, Lesk, Mae, Strand, Turn | Protein-oriented property schemes. |
| Nucleotide (DNA), Purine (DNA) | DNA-oriented schemes. |
| Identity to Consensus | Colors residues by identity with the per-column consensus. Aggregated overview cells show the fraction of matching residues. |
| Grayscale | Low-color overview. |
Residue Letters
| Control | Meaning |
|---|---|
| Letters | Shows or hides residue letters over the colored alignment cells. |
Turn letters off when zoomed out or when color blocks are more useful than individual residue labels.