msafara

msafara is a terminal-based viewer for multiple sequence alignments (MSAs). It provides a smooth interface to explore alignments directly from the command line — especially useful when working over SSH or in headless environments.

Installation

cargo install msafara

Quick Usage

Once installed, run:

msafara <my-alignment>

where my-alignment is a multiple alignment in FASTA, Clustal, or Stockholm format. If an unaligned FASTA is provided and mafft is configured, msafara will align it on load.

For help, run

msafara -h

Or press ? while running to see key bindings.

Features

Zoomed-in and zoomed-out views of the alignment
Consensus sequence display and conservation indicators
Sequence metrics such as ungapped length and similarity to consensus
Regex and EMBOSS motif search with live highlighting
Views for filtered/rejected subsets and selection-based exports
Tree-aware ordering and tree navigation (when available)
SVG export of the current view
Color maps for nucleotides and amino acids
Full keyboard control, no mouse required

Best results in a dark-themed terminal.

Configuration is read from .msafara.config (first in $HOME, then the current directory) for tool paths (EMBOSS/mafft) and color settings. Sessions can be saved as .msfr files and re-opened later.

More Info

Source, releases, and test data:
https://github.com/pmcarlton/msafara
Platform-specific binaries (Linux, macOS) available on the Releases page.

📝 License