aform-rs

Terminal-based Stockholm alignment editor for RNA, DNA, and protein sequences with vim-style modal editing.

Main editor view

Features

Vim-style editing - Modal editing with Normal, Insert, Visual, and Command modes
RNA/DNA/Protein support - Auto-detects sequence type with appropriate coloring
RNA structure - Base pair highlighting from SS_cons annotations
Color schemes - Structure, nucleotide, amino acid, conservation, and compensatory coloring
Annotation bars - Consensus sequence and conservation level visualization
Collapse identical - Group and collapse identical sequences
Block selection - Visual block mode for rectangular selections
Undo/redo - Full history with efficient copy-on-write sequences
Sequence clustering - Cluster sequences by similarity with dendrogram visualization

Clustering with Dendrogram

Cluster sequences by similarity and visualize relationships with an ASCII dendrogram tree.

Clustering with tree

Annotation Bars

Display consensus sequence and conservation levels below the alignment.

Annotation bars

Protein Support

Auto-detects protein sequences and applies amino acid coloring (Taylor scheme).

Protein alignment

Structure Coloring

Structure coloring mode

Visual Block Selection

Visual block selection

Quick Start

# Open a Stockholm file
aform alignment.stk

# With structure coloring
aform --color structure alignment.stk

# With amino acid coloring for proteins
aform --color protein alignment.stk

Press ? for help within the editor.