salti

A modern, multiple sequence alignment (MSA) viewer - built for the terminal.

Overview

salti is a standalone, self-contained terminal user interface (TUI) application designed for the browsing and inspection of multiple sequence alignments in FASTA format. The application operates entirely within the terminal environment, making it advantageous for HPC environments and/or remote servers where graphical user interfaces are unavailable or impractical.

Aiming to be feature rich, fast and optimised for large alignments - salti is under active development.

Current Features

• High performance: Able to load 10,500 mpox alignments in a few seconds
• Consensus calculation: Consensus is calcualted in the background for the visable alignment range
• Navigation: Quick navigation to specific alignment positions or sequence names
• Fuzzy sequence name search: Find sequences by name using fuzzy matching
• Supports DNA and AA alignments: Guesses file type (DNA/AA) and loads an appropriate colour scheme by default

Planned Features

• Amino Acid translation - Background translation of AA codons
• Support other file formats - Support other alignment file formats e.g phylip
• Extended colour schemes - e.g by identity
• Screenshots - Ability to export screenshots of current region
• Filtering - Filter records
• Options - Options widget to configure options in app

Demo

2025-06-10.21-32-34.mp4

Installation

Binaries

Binaries are attached to the latest release.

Building from Source

salti currently requires building from source:

Prerequisites

Install the Rust toolchain following the official documentation: Rust Installation Guide

Repository Setup

Clone the repository from GitHub:

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

Compilation and Installation

Build:

cargo build --release

The compiled executable will be located at salti/target/release/salti.

Usage

Basic Operation

Launch salti with a FASTA alignment file:

salti alignment.fasta

Optionally specify an initial position (1-based indexing):

salti alignment.fasta --position 150

Keyboard Controls

Application Controls

• q - Exit application
• ? - Toggle help widget
• j - Toggle jump widget

Navigation Controls

• ↑/↓ - Scroll vertically through sequences (one line at a time)
• ←/→ - Scroll horizontally through alignment positions (one column at a time)
• Hold Shift to scroll 10 at a time
• Home - Jump to alignment start position
• End - Jump to alignment end position
• c - Cycle colour modes

Consensus calculation

The consensus shows the most frequent nucleotide at each position, excluding gaps (-). Positions with no valid nucleotides display *.