Ale is an alignment editor for genetic sequences. It
Supports nucleic and amino acid sequences;
Provides a powerful vocabulary of alignment manipulation commands;
Can read and write alignments in GenBank, EMBL, Fast-A, and Phylip formats, in addition to its own format, designed for speedy access to large alignments;
Is free / open source software. This means that Ale is distributed with full source code, which you are guaranteed the right to modify and redistribute. You can support and extend Ale in-house, if you want.
Ale is built on top of GNU Emacs, and requires Emacs 24 or higher to run.
See our screenshots page for more.
In Memoriam Carl Woese
Ale was originally written in 1994-1995, as a project of the laboratory of Prof. Carl Woese at the University of Illinois at Urbana-Champaign and the laboratory of Prof. Norman Pace at the University of Indiana, Bloomington. It then lay dormant for about seven years, then perked up for a while, then went dormant again, then perked up a little bit, and now might or might not be dormant. You can download Ale here and try it out; if you run into any problems, or are interested in continuing Ale development, please contact Jim Blandy or Karl Fogel.
Download Ale 0.2.69 (prepackaged source code)
Ale is kept under version control using Subversion. You can browse the Ale repository, and if you have the "svn" client installed, you can check out a working copy of Ale like this:
svn co https://svn.red-bean.com/repos/ale/trunk ale
If you've just downloaded, built, and installed Ale, and now you're wondering how to try it, run this from the top of the Ale source tree:
Ale isn't the only genetic sequence written in Emacs and released as free software, believe it or not. There's also RALEE (RNA ALignment Editor in Emacs), by Sam Griffiths-Jones, which was written up in Oxford University's journal Bioinformatics, vol. 21, issue 2.
Also, the Debian GNU/Linux distribution lists a sequence editor called biomode, which mentions Emacs as a dependency.
Possibly search://emacs genetic sequence alignment/ would turn up more such packages. Please let us know if you see anything out there.