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:

Key Bindings

Navigation

Editing (Insert Mode)

Visual Mode (Block Selection)

In Normal mode, p pastes the yanked block at the cursor position, replacing characters in place.

Visual Line Mode (Sequence Selection)

Visual Line mode (V) selects complete sequences including their IDs and all annotations (#=GS, #=GR). When you yank with y, the clipboard contains a complete sub-alignment that can be used to create a new split pane (see Split Panes below).

Structure

Split Panes

Commands

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.

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. Protein alignments automatically enable base coloring, consensus, and conservation bar. RNA/DNA alignments with SS_cons automatically enable structure coloring. You can also manually set the type:

Annotation Bars

Toggle annotation bars below the alignment:

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.

Split Panes

aform-rs supports vim-style split panes for viewing and extracting sequences.

Basic Splits (Viewport Only)

Use Ctrl-w s (horizontal) or Ctrl-w v (vertical) to split the view. Both panes show the same alignment with independent scroll positions. Use Ctrl-w w or Ctrl-w + arrow keys to switch between panes.

Extracting Sequences to a New File

The real power of splits comes from combining Visual Line mode with splits to extract a subset of sequences:

1. Select sequences - Navigate to the first sequence you want, press V to enter Visual Line mode, then use j/k to extend the selection
2. Yank - Press y to copy. You'll see "Yanked X of Y sequence(s) [linewise]"
3. Split - Type :split or :vsplit. The new pane opens with only the yanked sequences
4. Save - In the new pane, type :w subset.sto to save the extracted sequences

The yanked sub-alignment includes: - Selected sequences with their IDs - All #=GS annotations for those sequences - All #=GR annotations for those sequences - All #=GC column annotations (SS_cons, RF, etc.) - All #=GF file annotations

Example Workflow

# Open a large alignment
aform alignment.sto

# Navigate to row 10
10G

# Enter Visual Line mode
V

# Select rows 10-15
5j

# Yank the 6 sequences
y

# Create split with yanked sequences
:split

# (Now in secondary pane with 6 sequences)
# Save to new file
:w subset.sto

# Close the split and return to original
:q

Split Commands