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Simple terminal sequence alignment viewer.


What is Alen?

It's a command-line program to view DNA or protein alignments in FASTA formats. Alen is meant for having a quick view of an alignment without having to leave the shell. It's not an alignment editor.

How to install and run.

Alen should work on most Unix systems, and Windows 10. If someone asks me to, I might add Windows 7 and 8 support.

The easiest way to get it is to download the latest release from the releases page (binaries are not yet available for Windows).

Alternatively, you can download the source code from this repo and compile it yourself using cargo build --release.

How to use

Simple usage:

$ alen /path/to/alignment.fasta

Note that Alen loads in the entire alignment into memory, so don't use it for multi-gigabyte files. Alen will auto-detect whether the alignment is a nucleotide or amino acid. For more help, type alen --help in the terminal.


  • Esc / q / Ctrl-C: Quit
  • c: Toggle consensus sequence comparison
  • r: Re-render the screen.
  • Ctrl-f: Find. Searches headers, then sequences for regex, case insensitively.
  • Ctrl-j: Jump to column.
  • Ctrl-s: Select rows and move them around.
  • Arrow keys: Move 1 column/row
  • Shift-Arrow keys: Move 10 columns/rows
  • Ctrl-Arrow keys: Move to first/last column/row



Why the name?

First, it's to pun on the unimaginative named alan and alv. Second, alen means cubit in Danish. Like using cubits, Alen is simple, crude, but usually good enough.