[BioPython] clustalw and trees
Peter
biopython at maubp.freeserve.co.uk
Thu Jul 26 13:55:14 UTC 2007
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
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