[Bioperl-l] Using Muscle parameter within bioperl

Albert Vilella avilella at gmail.com
Wed Dec 20 09:07:17 EST 2006

Try something like:

my @params =('verbose'=>0, 'quiet'=>1, 'log'=>'/tmp/inv.log');
my $factory = Bio::Tools::Run::Alignment::Muscle->new(@params);

it works for me with muscle 3.6. The log only gives me a start,
commandstring and end. I dunno if that is what muscle is supposed to
spit out.


On 12/19/06, Shrinivasrao P. Mane <smane at vbi.vt.edu> wrote:
> Hi,
> I need to run muscle using bioperl. This is how I do it in command line.
> muscle -in inv.fasta -out inv.aln -log inv.log -verbose -quiet
> I used the following in perl script
> my $muscle = new Bio::Tools::Run::Alignment::Muscle(-format =>
> 'clustalw',  -verbose=>'', -quiet=>'', -log='inv.log');
> The program runs and produces the result file but it doesn't create a
> log file nor does it stop sending output to STDOUT (-quiet).
> Could anybody help me with this?
> Thanks
> Mane
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