[BioPython] clustalw and trees

[Peter]

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