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

MIT