[EMBOSS] clustalw vs. emma

[Peter Rice]

Derek Gatherer wrote:

> In the docs http://emboss.sourceforge.net/apps/cvs/emma.html, there 
> are quite a few optional parameters of this sort, some of which work 
> and others don't, eg:

Yup - we're putting that right (some people have noticed the application docs 
are moving around).

The emboss.sf.net website only documents things for the latest code in CVS. We 
are adding documentation for release 3.0.0 (that is why the new directories 
are appearing).

The release 3.0.0 documentation is installed on your system when you install 
3.0.0 - if you install to /usr/local/bin it will be in:

/usr/local/share/EMBOSS/doc/programs/html (this will change in release 4.0.0).

You are seeing some of the changes made to make standard names for command 
line qualifiers since 3.0.0

Hope that helps,

Peter