[Biopython-dev] "Features" of Bio.Clustalw

[Davide Marchignoli]

I wanted to point out some (minor) problem I had using Bio.Clustalw.

In an alignment run clustalw generates two files:
- the output file (with default extension aln), and
- the tree file (with default extension dnd)
the MultipleAlignCL permits to change the output file with method
set_output but there is no way to change the tree file.

Is it possible to add a method set_tree that add to the command line the
-newtree option and the -align option (At the moment I am subclassing
MultipleAlignCL)?

The do_alignment function executes
  print "executing %s..." % command_line
and I think not everybody want it printed (I do not). Yes, one could
temporary redirect sys.stdout, but why?

Even if one sets the alignment type to PROTEIN (via set_type method of
MultipleAlignCL) the resulting alignment has DNA alphabet.

Tkanks, for your attention,

				Davide Marchignoli

PS: Is it possible to submit patches to biopython? How can I contribute?