[BioPython] clustalw and trees

[Michael Fahy]

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.

-----Original Message-----
From: Peter [mailto:biopython at maubp.freeserve.co.uk] 
Sent: Thursday, July 26, 2007 6:55 AM
To: fahy at chapman.edu
Cc: biopython at biopython.org
Subject: Re: [BioPython] clustalw and trees

Michael Fahy wrote:
> 
> Speaking of the clustalw command line, is it possible to get clustalw to
> output a phylogenetic tree file, rather than an alignment file, via
> command line arguments?

Do you mean in addition to the guide tree (*.dnd) it generates by 
default when building an alignment (*.aln) from a fasta input?

I would have a look at clustalw -help (which works on Linux!) for more 
options, e.g.

-OUTPUTTREE=nj OR phylip OR dist OR nexus
-SEED=n        :seed number for bootstraps.
-KIMURA        :use Kimura's correction.
-TOSSGAPS      :ignore positions with gaps.
-BOOTLABELS=node OR branch :position of bootstrap values in tree display

Peter