Re: [Dart-help] Code for EM algorithm for training Hidden Subst models

[Ian H. <ih...@be...>]

Vincent Yan Fu Tan wrote:
> Dear Prof. Holmes,
>
> I read your paper on an EM algorithm for Training Hidden Substitution
> Models. In it you mentioned that there's freely available code under
> the GNU Public License at www.biowiki.org/hsm. However, this link
> appears to be broken. I was wondering whether you can fix the link or
> send me a copy of the code for research purposes.
>
> Thanks and best regards,
> Vincent
>

Hi Vincent,

The biowiki.org website appears to be very slow at the moment -- this
occurs periodically, I think because I haven't excluded web robots
correctly so it's currently being pounded by Google/Yahoo/Bing... sigh.
It seems to recover in an hour or two.

Anyway, the link (biowiki.org/hsm) should redirect to biowiki.org/DART,
which is where all my molecular evolution software is distributed at the
moment. The particular program you want is XRATE, which is described at
biowiki.org/XRATE

Even if biowiki.org is down, you can get the code itself from here:
http://github.com/ihh/dart/tree/master

Do let me know if you have other questions...

Best wishes,
Ian