[Debian-med-packaging] embassy-phylip_3.68-1_amd64.changes is NEW

[Charles Plessy]

Le Sat, Aug 08, 2009 at 04:34:52PM +0200, Andreas Tille a écrit :
> On Sat, Aug 08, 2009 at 01:02:04PM +0000, Archive Administrator wrote:
> >  PHYLIP (the PHYLogeny Inference Package) is a package of programs for
> >  inferring phylogenies (evolutionary trees). Methods that are available
> >  in the package include parsimony, distance matrix, and likelihood
> >  methods, including bootstrapping and consensus trees. Data types that
> >  can be handled include molecular sequences, gene frequencies,
> >  restriction sites and fragments, distance matrices, and discrete
> >  characters.
> >  .
> >  The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them
> >  from the original programs and avoid namespace conflict.
> 
> What exactly is the difference between phylip and embassy-phylip?
> I did not got it out of the description.  Could some command line switch
> or something like this which might be acceptable by phylip authors and
> that way avoid potential duplication of code?

Embassy-philip provides the same functionalities but with an emboss command
line interface, which gives the possibility to get sequences directly from
databases, for instance. The embassy-phylip have a prefix to their name, so
both versions can be installed together. I have seen at least one phylogeny
pipeline that was specifically depending on embassy-phylip. I was about to use
it last week, which is why I took opportunity to close this old ITP bug.

I do not think that we can do much for the code duplication, but it is very
unlikely that it causes us some problems.

Have a nice day,

-- 
Charles