View Alignments

In development

This feature is not yet in a SEGUL release. It will be available in the next SEGUL release. Commands and key bindings may change before the release.

View alignments in an interactive viewer right in your terminal. It works like the SEGUI alignment viewer (in development). It is handy for checking alignments on a remote server or in a terminal session where a GUI is not available.

To view an alignment, use the following command:

segul view align --input alignment.fasta

It is designed to be fast and can handle large alignments efficiently.

Input formats

For the best efficiency, use FASTA format.

Layout

From top to bottom, the viewer shows:

1. Toolbar: the file name, the number of taxa and sites, the data type (DNA or amino acid), whether the sequences are unaligned, the color mode, the zoom level, and the current chunk.
2. Overview: a strip showing the whole alignment, with a line marking the sites in view. Click or drag on it to jump.
3. Legend: the residue colors. DNA shows A, C, G, and T. Amino acids show the Clustal X groups: hydrophobic, positive, negative, polar, aromatic, glycine, proline, and cysteine.
4. Taxon names and residue grid: the names on the left, a ruler with site numbers on top, and the colored residues. Chunk boundaries are marked on the ruler.
5. Status bar: the taxon, site, ungapped position, and residue under the cursor.

Press Ctrl+B to show the chunk sidebar. It lists each chunk of sites with its share of gaps and variable sites.

Detailed usage

Viewing several alignments

Pass several files, or a directory, to switch between them in the viewer:

segul view align --dir alignments/

segul view align --input alignments/*.nex

Use Ctrl+PgDn and Ctrl+PgUp to move to the next or previous file, or Ctrl+P to pick a file from a searchable list. Settings such as zoom and color mode carry over when you switch files.

Data type

SEGUL detects whether the sequences are DNA or amino acids from the residues. This is the default (--datatype ignore), unlike other SEGUL commands. To set the data type yourself, use --datatype dna or --datatype aa:

segul view align --input alignment.fasta --datatype aa

Colors and terminal themes

The residue colors are made for dark terminals. If your terminal has a light background, use --theme light:

segul view align --input alignment.fasta --theme light

Terminals that support 24-bit color show the exact SEGUI colors. Other terminals show the nearest of 256 colors. Most modern terminals support 24-bit color and report it with the COLORTERM environment variable.

Press F2 to cycle the color modes:

• Base: each residue in its own color.
• Mono: one color for residues and another for gaps.
• Diff to first: residues that match the first sequence are shown as dots, so differences stand out.

Chunks

The viewer splits the alignment into chunks of 1,000 sites by default. Use --chunk to pick 250, 500, 1000, or 2000 sites per chunk:

segul view align --input alignment.fasta --chunk 500

Use [ and ] to move between chunks. Press Ctrl+K then P to show one chunk at a time.

Selecting and copying sequences

Press Space to select the sequence under the cursor, Shift+↑ or Shift+↓ to extend the selection, and Ctrl+A to select all. Then:

• Ctrl+C copies the selected sequences as FASTA to the clipboard. This uses the terminal's clipboard support (OSC 52), which works in most modern terminals, including over SSH.
• Ctrl+S saves them as <file name>-selected.fas in the current directory.

With no selection, both act on the sequence under the cursor.

Key bindings

The key bindings follow Visual Studio Code. Press F1 or ? in the viewer to see them.

Windows and Linux	macOS	Action
← ↑ → ↓	← ↑ → ↓	Move the cursor
Ctrl+← / Ctrl+→	Option+← / Option+→	Jump 10 sites
Home / End	fn+← / fn+→	First / last site of the sequence
Ctrl+Home / Ctrl+End	Ctrl+fn+← / Ctrl+fn+→	First / last taxon
PgUp / PgDn	Option+↑ / Option+↓	Page through taxa
Alt+PgUp / Alt+PgDn	Option+Shift+← / →	Page through sites
[ / ]	[ / ]	Previous / next chunk
Ctrl+G	Ctrl+G	Go to a site (120), a taxon, or taxon:120
Ctrl+F	Ctrl+F	Find a taxon by name
Enter or F3	Enter or fn+F3	Next match (Shift for the previous one)
+ / - / Ctrl+0	+ / - / Ctrl+0	Zoom in / out / reset
F2 or Ctrl+K C	Ctrl+K C	Cycle color mode
F4 or Ctrl+K L	Ctrl+K L	Show or hide residue letters
Ctrl+K P	Ctrl+K P	Show one chunk at a time
Ctrl+B	Ctrl+B	Show or hide the chunk sidebar
< / >	< / >	Narrow / widen the taxon names
Space / Shift+↑ ↓	Space / Shift+↑ ↓	Select a sequence / extend the selection
Ctrl+A	Ctrl+A	Select all sequences
Ctrl+C	Ctrl+C	Copy selected sequences as FASTA
Ctrl+S	Ctrl+S	Save selected sequences as FASTA
Ctrl+PgUp / Ctrl+PgDn	Ctrl+fn+↑ / Ctrl+fn+↓	Previous / next file
Ctrl+P	Ctrl+P	Pick a file
F1 or ?	?	Show key bindings
Ctrl+Q or Esc	Ctrl+Q or Esc	Quit (Esc first closes any open prompt)

You can also use the mouse. Scroll to move through taxa, hold Shift while scrolling to move through sites, and hold Ctrl while scrolling to zoom. Click a residue to move the cursor, click a taxon name to select it (Shift-click to select a range), and drag the line next to the names to resize them.

macOS terminal settings

• Option keys: if Option+← types a character or does nothing, let Option act as a modifier. In Terminal, open Settings → Profiles → Keyboard and turn on Use Option as Meta key. In iTerm2, open Settings → Profiles → Keys and set Left Option key to Esc+.
• fn keys: Terminal scrolls its own window with fn+↑, fn+↓, fn+←, and fn+→. Add Shift (for example Shift+fn+↑) to send them to the viewer, or use Option+↑ and Option+↓ to page.
• Function keys: on Mac keyboards, F1 to F4 need fn unless the function keys are set as standard function keys. The viewer offers ?, Ctrl+K C, and Ctrl+K L instead.

Note

Some terminals use Ctrl+= or Alt shortcuts for their own features. If a shortcut does not work, use the alternative in the table, such as + and - for zoom or Ctrl+K C for colors.

All options

Option	Description
-d, --dir	Directory with alignments
-i, --input	Alignment files. Allows wildcards
-f, --input-format	Input format: auto (default), fasta, nexus, or phylip
--datatype	Data type: ignore (default, detects DNA or amino acids), dna, aa
--theme	Colors for a dark (default) or light terminal
--chunk	Sites per chunk: 250, 500, 1000 (default), or 2000