[Bioperl-l] Re: Phylip question

shawnh@fugu-sg.org shawnh@fugu-sg.org
Tue, 5 Nov 2002 23:39:28 +0800 (SGT)

I wrote a couple of wrappers only for a couple of Phylip programs.
They can be found in the bioperl-run package under


with only ProtPars, Neighbor, and ProtDist written.
It only supports 3.5 and not the 3.6 alpha version although I haven't 
tested it. But I suspect some of the interactive menus might have changed
so it will need tweaking to work with 3.6.

In anycase, ProtDist takes in a Bio::SimpleAlign object from which you can
generate using Bio::Tools::Run::Clustalw passing in an array of sequences.
This creates a distance matrix. With this you can create a parsimony tree 
using the ProtPars wrapper which returns you a Bio::Tree object.
Alternatively  you can use Neighbor passing in the matrix as well which also
returns a Bio::Tree.

The wrappers makes use of the following set of modules for parsing:

Bio::AlignIO which allows you to work with phylip formats,
transforming Bio::SimpleAlign objects to and from PHYLIP interleaved format.

Bio::TreeIO which allows you to parse newick formats among others.

hope that helps.



On 5 Nov 2002, Heikki Lehvaslaiho wrote:

> David,
> In bioperl we do not deal directly with PHYLIP programs but what we have
> is a generic interface to free EMBOSS program suite and there is a
> version of PHYLIP that uses the EMBOSS interface. Check
> http://www.emboss.org/.
> The bioperl modules to use are:
> Bio::Factory::EMBOSS
> Bio::Tools::Run::EMBOSSApplication
> We have nothing that would help you process the output from PHYLIP
> programs. Contributions would be more than welcome.
> Hope this helps,
> 	-Heikki
> On Tue, 2002-11-05 at 00:29, Dave Lee wrote:
> > Heikki,
> >  
> > Hi, my name is David and I'm working on a research project at Berkeley.
> > I'm wondering if you can help me out a little bit. I saw that you wrote
> > phylip.pm and so I thought I'd give you an email. If you can't help,
> > then could you point me to another resource? Thanks.
> >  
> > What I want to do is write a PERL program that takes arrays of
> > nucleotides and uses the PHYLIP programs to produce a distance matrix
> > and phylip tree info. Has anyone already written a similar PERL program
> > that does this? It would save me much time.
> >  
> > Thanks for your prompt reply,
> > -Dave
> > Bioinformatics Researcher
> > Bioengineering, University of California at Berkeley

* Shawn Hoon
* http://www.fugu-sg.org/~shawnh