Usage
Opening Files
aform alignment.stk
aform --color structure alignment.stk
aform --cluster --tree --conservation alignment.stk
Use :e <path> to open files from within the editor (Tab completes paths).
Modes
aform-rs uses vim-style modal editing:
| Mode | Enter | Description |
|---|---|---|
| Normal | Esc |
Navigation and commands |
| Insert | i |
Edit sequence characters |
| Visual | v |
Block selection |
| Command | : |
Ex-style commands |
| Search | / |
Pattern search |
Key Bindings
Navigation
| Key | Action |
|---|---|
h/j/k/l |
Move cursor |
0 / $ |
Line start/end |
gg / G |
First/last sequence |
Ctrl-f/b |
Page down/up |
Ctrl-d/u |
Half page down/up |
w / b |
Jump 10 columns right/left |
Editing (Insert Mode)
| Key | Action |
|---|---|
a-z, A-Z |
Insert nucleotide |
-, . |
Insert gap |
Backspace |
Delete character |
Visual Mode
| Key | Action |
|---|---|
v |
Enter visual mode |
y |
Yank (copy) selection |
d / x |
Delete selection |
Esc |
Exit visual mode |
In Normal mode, p pastes the yanked block.
Structure
| Key | Action |
|---|---|
gp |
Go to base pair partner |
[ / ] |
Previous/next helix |
Commands
| Command | Description |
|---|---|
:w |
Save file |
:q |
Quit |
:wq |
Save and quit |
:e <path> |
Open file (Tab completes path) |
:color <scheme> |
Set color scheme |
:trim |
Remove gap-only columns (both ends) |
:trimleft |
Remove leading gap-only columns |
:trimright |
Remove trailing gap-only columns |
:upper |
Convert to uppercase |
:lower |
Convert to lowercase |
:t2u |
Convert T to U |
:u2t |
Convert U to T |
:noh |
Clear search highlighting |
:cluster |
Cluster sequences by similarity |
:uncluster |
Restore original sequence order |
:tree |
Toggle dendrogram tree display |
:collapse |
Toggle collapse of identical sequences |
:consensus |
Toggle consensus sequence bar |
:conservation |
Toggle conservation level bar |
:ruler |
Toggle column ruler |
:rownum |
Toggle row numbers |
:shortid |
Toggle short IDs (strip /start-end suffix) |
:type <type> |
Set sequence type (rna/dna/protein/auto) |
Clustering
Cluster sequences by pairwise similarity using :cluster. This reorders sequences using hierarchical agglomerative clustering (UPGMA algorithm with Hamming distance), grouping similar sequences together.
Use :tree to show a dendrogram alongside the alignment, visualizing sequence relationships. The tree uses ASCII box-drawing characters and adapts to your terminal's color scheme.
To restore the original sequence order, use :uncluster.
Color Schemes
Set with :color <scheme> or --color flag.
| Scheme | Aliases | Description |
|---|---|---|
none |
off |
No coloring |
structure |
ss |
Color by helix (rainbow) |
base |
nt, protein, aa, residue |
Color by nucleotide or amino acid |
conservation |
cons |
Color by column conservation |
compensatory |
comp |
Highlight compensatory mutations |
The base scheme automatically uses nucleotide colors for RNA/DNA or amino acid colors (Taylor scheme) for protein sequences based on auto-detection.
Sequence Type
aform-rs auto-detects the sequence type (RNA, DNA, or Protein) when loading a file. You can also manually set it:
| Command | Description |
|---|---|
:type |
Show current sequence type |
:type rna |
Set to RNA |
:type dna |
Set to DNA |
:type protein |
Set to Protein |
:type auto |
Auto-detect from alignment |
Annotation Bars
Toggle annotation bars below the alignment:
| Command | Description |
|---|---|
:consensus |
Show consensus sequence (uppercase = high conservation) |
:conservation |
Show conservation level with height-varying bars (▁▂▃▄▅▆▇█) |
Collapse Identical Sequences
Use :collapse to group identical sequences together, showing only one representative with a count indicator (e.g., seq1 (5) means 5 identical sequences). This reduces visual clutter in alignments with many duplicates.