title: TERMAL subtitle: A TUI multiple alignment viewer author: Thomas Junier

Summary

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

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

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
• consensus sequence
• residue colouring
• representation of conservation

Motivation

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 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. Termal allows you to

Secondary

Example

$ termal data/aln4.pep

┌──┌───────────┌ data/aln4.pep - 16/16s (1.00) x 70/561c (0.12) - ────────────────────┐
│ 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 appears in monochrome due to 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.

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