Summary

Termal is a program for examining multiple sequence alignments in a terminal.

• No installer (just download and uncompress)
• No dependencies
• Best results in a terminal that supports 24-bit ("true color") color output

Quick Start

Download the latest archive, uncompress it, and run the binary on the example alignment (see below). Press "?" for help.

Linux (x86_64)

• Download

tar -xzf termal-v1.1.0-linux-x86_64.tar.gz
./termal data/example-1.msa

Windows

• Download

1. Unzip the archive
2. Open a terminal and run:

termal.exe example-1.msa

macOS

• Download

tar -xzf termal-v1.1.0-macos-x86_64.tar.gz
./termal data/example-1.msa

Tested on:

• Linux (EndeavourOS Build-ID 2024-01-15)
• macOS 10.13.6 (High Sierra)
• Windows 11

Synopsis

Just pass your alignment as argument to the termal binary:

$ termal [options] <alignment>

Interface

termal runs in a terminal and is entirely keyboard-driven.

Key Bindings

To see the key bindings while running termal, press "?". To display them in the console, run termal -b. The main bindings are as follows:

Motion

arrows: scroll 1 column/line; shift-arrows : scroll 1 screenful h,j,k,l are aliases for left, down, up, and right arrow ^,G,g,$: full left, bottom, top, full right

Zooming

z,Z: cycle through zoom modes

Adjusting the Panes

<,>: widen/narrow label pane a : hide/show label pane c : hode/show consensus pane f : toggle fullscreen alignment pane

Video

s: next color scheme m: next color map i: toggle inverse/direct video

Try dark/inverse for best results (this is the default).

Metrics and Orderings

o: next ordering t: next metric

Features

Termal has the basic features you'd expect of an alignment viewer, such as:

• moving and jumping around
• zoomed in or zoomed-out (whole alignment) views (see Zooming below)
• consensus sequence
• residue coloring
• representation of conservation

Zooming

By default, Termal shows as much of the alignment as fits on the screen. Smaller alignments can fit entirely on screen, but it's quite common for alignments to be too large, at least in one dimension, sometimes both. To see more of the alignment, there are two options:

• Scrolling: this simply shifts the displayed portion ("view port") of the alignment left, right, up, or down. One can move by a single line (sequence) or column (position), by screenfuls, or directly to the top, bottom, leftmost, or rightmost positions. This is done with the motion keys, including arrows

• Zooming Out: this shows the first and last sequences, as well as evenly-spaced sequences in between so as to show as many sequences as possible. The same sampling is applied to columns. A box shows the location of the view port, that is, what part of the alignment would fill the alignment area when zooming back in. The zoom box can be moved using the same commands as for scrolling (see above). A variant of zooming out will sample rows and columns will preserve the aspect ratio of the alignment, at the expense of potentially fewer sequences or columns shown.

Colors and Themes

The program was developed and tested in a dark-themed terminal, but it works reasonably well in light themes. It also has a monochrome "theme", which adapts to the theme (white on black in a dark theme, and the other way around). Press s to move from dark to light to monochrome (and back).

Termal can map residues to colors (except in monochrome mode) using one of the built-in color maps. The default color map is Clustal's for amino acids, and JalView's for nucleotides. Press m to change color maps.

By default, residues are colored in inverse video, as is done by most alignment viewers, but direct video is also possible. The i key toggles between the video modes.

Example

$ termal data/aln4.pep

┌──┌───────────┌ data/aln4.pep | 16/16s x 70/561c | Dark Mono White | Zoomed in ──────┐
│ 1│Abro_00865 │ELTDGFHLIIDALKLNGLNTIYGVPGIPITDFGRMAQAEGIRVLSFRHEQNAGYAASIAGFLTK-KPGVC│
│ 2│Aoxa_03215 │NLTDGFHALIDAFKKNDINNIYAVAGIPITDVLRLAVEREMKVIAFRHESNAGHAAAIAGYLTQ-KPGIC│
│ 3│Bden_01758 │ELTDGFHLVIDAMKLNGIDTIYNVPGIPITDLGRMAQAEGIRVLSFRHEQNAGYAAAIAGFLTK-KPGVC│
│ 4│Bphy_06740 │ETTDGFHLVIDALKLNDIKTIFGLVGIPITDLARLAQAEGMRFIGFRHEQHAGNAAAVSGYMTK-KPGIC│
│ 5│Bsp1_02714 │ELTDGFHLVIDALKLNGIDTVYGVPGIPITDLGRMAQAAGIRVLSFRHEQNAGYAASIAGFLTK-RPGVC│
│ 6│Cnec_05522 │AQTDGFHLVIDALKLNGIENIYGLPGIPVTDLARLAQANGMRVISFRHEQNAGNAAAIAGFLTQ-KPGVC│
│ 7│Cox1_00651 │AQTDGFHLVIDALKLNGIENIYGLPGIPVTDLARLAQANGMRVISFRHEQNAGNAAAIAGFLTQ-KPGVC│
│ 8│Cox2_00498 │AQTDGFHLVIDALKLNGIENIYGLPGIPVTDLARLAQANGMRVISFRHEQNAGNAAAIAGFLTQ-KPGVC│
│ 9│Mmas_01638 │ALTDGFHLVIDALKLNGINTIYDVPGIPISDLLRMAQAEGMRVISFRHEQNAGNAAAIAGFLTK-KPGVC│
│10│Msp1_01810 │ELTDGFHLVIDALKLNGIDTIYGVPGIPITDLGRMCQEEGMRVISFRHEQNAGNAAAIAGFLTK-KPGIC│
│11│Ofo1_01671 │ELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHEQHAGYAASIAGYIEG-KPGVC│
│12│Ofo2_00503 │ELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHEQHAGYAASIAGYIEG-KPGVC│
│13│Ofo3_01693 │ELTDGFHVLKDTLKLNGIDTMYGVVGIPITNLARLWEQDGQKFYSFRHEQHAGYAASIAGYIQGDKPGVC│
│14│Osp1_01723 │ELTDGFHVLKDVLKVNGIDTMYGVVGIPITNLARLWEQDGQKFYSFRHEQHAGYAASIAGYIHGDKPGVC│
│15│Osp2_01577 │ELTDGFHVLMDTLKMNDIDTMYGVVGIPITNLARLWEQDGQKFYSFRHEQHAGYAASIAGYIQGDKPGVC│
│16│Osp3_01912 │ELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARLWQDDGQRFYSFRHEQHAGYAASIAGYIEG-KPGVC│
└──└───────────└🬹🬹🬹🬹🬹🬹🬹🬹🬹═══════════════════════════════════════════════════════┘
│              │|    :    |    :    |    :    |    :    |    :    |    :    |    :    │
│Position      │0        10        20        30        40        50        60        7│
│Consensus     │elTDGFHlvIDALKlNgIdtiYGvpGIPITdLaRlaqadGmrviSFRHEQnAGyAAaIAGyltk-KPGVC│
│Conservation  │▅▅█████▄▄▆█▆▆█▄█▅▇▃▆▄▇▅▆▄███▆▇▅▆▄█▅▄▅▃▂▇▄▆▅▄▆████▇▅██▄██▅▇▇█▅▄▄▃▁▇██▆█│
└──────────────└──────────────────────────────────────────────────────────────────────┘

Notes

1. The above example shows termal in monochrome mode due to limitations in Markdown rendring, but by default Termal uses colours, e.g. to reflect amino acid chemistry.
2. The above example had to be slightly tweaked because the separation line between the main and bottom panel is rendered too wide in some Markdown engines.

Motivations

Primary

Multiple sequence alignments often reside on distant machines like HPC clusters, for two reasons:

1. They may require nontrivial resources to compute (this is especially true of large alignments);
2. They may serve as inputs to heavy-duty analyses like computing phylogenetic trees.

Like for any other input data, it's a good idea to have a quick look at an alignment before it is fed to an analysis pipeline. There are many fine tools for doing this, but most of them have a graphical user interface, so they (usually) can't be used over SSH. A multiple sequence alignment is basically just text, so it is well suited for a text interface.

Secondary

Even on a local machine, there are use cases for viewing alignments in a terminal, such as:

• Short load times: Rust programs can be very fast, and it is convenient to be able to have a quick look at an alignment without waiting several seconds for the program and alignment to load.
• Not needing to leave one's work environment - use termal on an alignment like you would use less, bat, etc. on any text file.

BUGS AND LIMITATIONS

• Currently, Termal can only read Fasta alignments (i.e., no Phylip or other formats).

LICENSE