[ssml] Re: Multiple sequence alignment

[Eric Pettersen]

> From: Barnali Chaudhuri <neel at mbi.ucla.edu>
> Subject: [ssml] Multiple sequence alignment
> To: ssml-general at bioinformatics.org
> Message-ID: <Pine.LNX.4.58.0507312251270.24473 at ewald.mbi.ucla.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>
> Hi all,
>
> How can I "quickly" evaluate the significance of a
> multiple sequence alignment (using entropy or some such)?
>
> Thanks
>
> Neel

I guessing you mean computing column conservation.  The program AL2CO  
provides a variety of such measures, including entropy.  ftp:// 
iole.swmed.edu/pub/al2co

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu