[BioPython] clustalw and trees

[Peter]

Michael Fahy wrote:
> Peter,
> 
> I was hoping to get it to generate a "real" phylip tree file rather than the
> guide tree that it generates automatically.  If I run it from the command
> line and add the flag "-OUTPUTTREE=phylip", it creates a guide tree file
> and an alignment file but no phylip tree file.  If I run it interactively I
> can get it to create a phylip tree file (which is different from the guide
> tree file) but I have not been able to figure out how to do this from the
> command line.

Oh. Maybe you need to pore over the clustalw documentation...

You might also look at the EMBOSS version of PHYLIP and use that instead 
(assuming its available on your OS).

http://emboss.sourceforge.net/apps/release/5.0/embassy/phylip/
http://emboss.sourceforge.net/apps/release/5.0/embassy/phylipnew/

They have repackaged all the PHYLIP tools with usable command line 
interfaces - if you have ever tried to use the original PHYLIP tools in 
a script you'll appreciate the difference.

Peter