salti

salti is a terminal based multiple sequence alignment (MSA) viewer for FASTA files. It is designed for fast interactive browsing primarily on remote servers, and HPC environments, or anytime you dont want to leave the terminal.

Contents

• Features
• Installation
• Usage
• Some notes on features

Features

Fast

salti is built for fast browsing and loading of large alignments, using tokio for async processing. This is in part achieved by:

• Background threads handle tasks such as consensus/conservation calculation and file loading, allowing these to complete dynamically without blocking the UI.
• Rendering only the visible portion of the alignment, updating the view on state changes rather than every frame tick, and caching consensus and conservation calculations in a window around the currently visible region.

It can handle alignments with thousands of sequences and >200,000 positions without lag (tested with ~3k mpox alignments)

Transparent support for HTTP/SSH/Compressed files

Thanks to the cool Paraseq library salti can transparently load compressed fasta files, as well as files over HTTP/HTTPS or SSH. Just provide the URL or SSH path to the load command, e.g. :load https://example.com/alignment.fasta or :load ssh://user@host/path/to/alignment.fasta.

Command palette

Press : to open a command palette for most actions. See Usage for details.

Mouse support

Left click to select a sequence/position, Ctrl+left click to select a region.

Hold middle mouse to pan around the alignment.

Minimap

Press m to open the minimap and drag to quickly pan around.

Nucleotide and Amino acid support

salti automatically detects whether your alignment is nucleotide (NT) or amino acid (AA), then applies the correct rendering mode.

Translation

Can translate NT codons to AA on the fly, with support for all 3 frames, although designed for browsing, rather than a dedicated translation tool.

Useful viz tools

• Collapse positions that match the reference or consensus to . for easier visualisation of differences.
• Mouse selection to highlight regions or sequences
• Pin important sequences fixed at the top while browsing.

Themes

salti supports multiple colour themes, which can be switched with the set-theme command. Available themes so far are:

• everforest-dark - the default theme, based on the everforest colorscheme.
• solarized-light - a light theme based on the solarized palette.
• tokyo-night - a dark theme based on the tokyo night palette.
• terminal-default - uses terminal-provided ANSI colours and defaults.

Installation

Conda:

conda install -c bioconda salti

Binaries:

Precompiled binaries for Linux, MacOS and Windows are attached to the latest release.

Cargo:

Requires cargo

cargo install salti

Build from source:

Install rust toolchain:

To install please refer to the rust documentation: docs

Clone the repository:

git clone https://github.com/Sam-Sims/salti

Build and add to path:

cd salti
cargo build --release
export PATH=$PATH:$(pwd)/target/release

All executables will be in the directory salti/target/release.

Usage

I would recommend a modern terminal, with GPU acceleration and 24-bit colour (true colour) support for the best experience. Additionally, a font with Unicode support is required to render all characters correctly.

I would also recommend a large terminal window for the best experience, but the app is designed to be usable even in smaller windows.

salti is primarily developed and benchmarked in Ghostty. I have tested it on several other terminals and it works well in most cases, though performance may vary. If you have responsiveness issues, please open an issue and include your terminal emulator and font information.

salti <alignment.fasta>

If no file is passed, the app starts and waits for you to load one via the command palette.

Quick start keybinds

I plan to add a help screen in the future for reference in app, but for now here are the most useful keybindings:

Global keybindings

• q - Quit.
• : - Opens the command palette.
• Up / Down - Scroll vertically 1 row
• Left / Right - Scroll horizontally 1 column.
• Shift + Left/Right/Up/Down scrolls 10 columns/rows in that direction.
• Alt+Left / Alt+Right - Scroll sequence name pane.
• Left cick - Select a sequence or position. Click again to clear selection.
• Ctrl + Left click - Select a range of sequences or positions
• Middle click + drag - Pan.
• m - Open the minimap

Command palette

Most features can be accessed through the command palette (this is heavily inspired by the helix editors implementation!).

Open with :, then type a command.

• Enter confirms selection.
• Tab / Shift+Tab cycles any candidates.
• Esc closes the palette.

Commands:

• jump-position - Jump to a 1-based alignment position.
• jump-sequence - Jump to a sequence by name
• pin-sequence - Pin a visible sequence to the top of the alignment view.
• unpin-sequence - Remove a sequence from the pinned group.
• set-filter - Filter visible sequences by regex.
• clear-filter - Clear the active filter.
• set-reference - Set a reference sequence .
• toggle-translate - Toggle AA translation.
• set-diff-mode - Set diff rendering mode (off, reference, or consensus).
• load-alignment (alias: load) - Load an alignment file.
• set-consensus-method - Choose majority or majority-non-gap.
• set-translation-frame - Set translation frame (1, 2, or 3).
• set-theme - Set active theme (everforest-dark, solarized-light, tokyo-night, or terminal-default).
• set-sequence-type - Override auto-detection if it fails (dna, aa, or full).
• check-update - Check for updates and show the latest version.
• quit - Quit the app.

Some notes on features

Fuzzy matching

All commands that take string input support fuzzy matching. For example, jump-sequence will match any sequence name that contains the input string. If multiple candidates match, you can cycle through them with Tab / Shift+Tab.

Consensus method

Two methods are available for consensus calculation:

• majority - The most common character at each position, including gaps.
• majority-non-gap - The most common character at each position, excluding gaps

If there is a tie for most common character, one is chosen at random.

Consensus is calculated in the background

Pinned behaviour

• Pinned sequences stay visible and remain at the top, even when they do not match the active filter.
• Setting a sequence as reference removes it from pinned state and hides it as the reference row.

Data/Rendering

• Input must be FASTA with equal sequence lengths across records.
• Sequence type is auto-detected on load; you can override it if its wrong.
  • It samples up to 100 random alignments and compares NT and AA character fractions. If neither crosses 50%, it falls back to full mode.

Update check:

salti will check for updates on startup and notify you if a new version is available. It does this by querying the crates api: https://crates.io/api/v1/crates. However, no network connection is required, and will not cause any issues if the check fails.

This behaviour can be disabled entirely by setting SALTI_SKIP_UPDATE_CHECK=true. You can still check for updates manually with the check-update command.