https://github.com/jakobnissen/alen

Simple terminal alignment viewer
https://github.com/jakobnissen/alen

Last synced: 4 months ago
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Simple terminal alignment viewer

• Host: GitHub
• URL: https://github.com/jakobnissen/alen
• Owner: jakobnissen
• License: mit
• Created: 2021-06-22T18:27:03.000Z (about 3 years ago)
• Default Branch: master
• Last Pushed: 2023-12-07T11:22:26.000Z (7 months ago)
• Last Synced: 2024-01-17T00:49:42.120Z (6 months ago)
• Language: Rust
• Size: 399 KB
• Stars: 66
• Watchers: 6
• Forks: 3
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• awesome-genome-visualization - alen
• repo-5916-awesome-genome-visualization - alen - genome-visualization/alen.png) (MSA)

README

        
# Alen

Simple terminal sequence alignment viewer.

![Screenshot](/screenshots/prot.png?raw=true "Screenshot")

### 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](https://github.com/jakobnissen/alen/releases) (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.

__Commands__

* `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

### Configuration

No.

### Why the name?

First, it's to pun on the unimaginative named [alan](https://github.com/mpdunne/alan) and [alv](https://github.com/arvestad/alv). Second, _alen_ means _cubit_ in Danish. Like using cubits, Alen is simple, crude, but usually _good enough_.