[Bioperl-l] Bio::Tools::Run::Alignment::Clustalw

[Josh Lauricha]

I have a small patch for Clustalw.pm to allow the creation of trees
without multiple alignments. But, of course, I've got a few questions ;)

One thing that bothers me with Clustalw.pm is that its not quiet by
default. I'd rather not see the garbage from clustalw, and having it
print out a bunch of stuff is not what I expected, is it ok if I change
it to be quiet by default?

Theres a chmod in _run, why is that there? and why is it setting it
group and world readable? Shouldn't permissions be delegated to the OS?

Since the tree is generated with a multiple alignment (and I wanted one
of those too), I'd like to make an option to save the tree. However,
align() returns the alignment... Should I add "{save,get}_tree" or have
it return the tree if wantarray is set? I think the last is the most
natural, and lets the module clean up after itself easily.

Thanks,

-- 

----------------------------
| Josh Lauricha            |
| laurichj at bioinfo.ucr.edu |
| Bioinformatics, UCR      |
|--------------------------|