[Bioperl-l] Bio::Tools::Run::Alignment::MAFFT - specifying alignment parameters

[Dr. Oliver Niehuis]

Hi,

I have a question about how to specify parameters for the alignment  
program MAFFT via the Bio::Tools::Run::Alignment::MAFFT module. I  
would like to run MAFFT with the following alignment parameters:

--maxiterate 1000 --localpair

Having used TCOFFEE and the Bio::Tools::Run::Alignment::Tcoffee module  
before, I specified the MAFFT run parameters as follows:

@params = ('localpair', 'maxiterate' => 1000);
$factory = Bio::Tools::Run::Alignment::MAFFT->new(@params);

Unfortunately, this code causes an exception error:

------------- EXCEPTION -------------
MSG: Unallowed parameter: LOCALPAIR !
STACK Bio::Tools::Run::Alignment::MAFFT::AUTOLOAD /sw/lib/perl5/5.8.8/ 
Bio/Tools/Run/Alignment/MAFFT.pm:211
STACK Bio::Tools::Run::Alignment::MAFFT::new /sw/lib/perl5/5.8.8/Bio/ 
Tools/Run/Alignment/MAFFT.pm:196
STACK toplevel /Users/Oliver/Desktop/Orthologs/ 
Generate_FASTA_files_of_orthologs.pl:55
-------------------------------------

I can align sequences with MAFFT via Bio::Tools::Run::Alignment::MAFFT  
module, but only when leaving the @params array empty; MAFFT then runs  
with the default parameters.

Has anyone an idea how I can specify run parameters for MAFFT via the  
Bio::Tools::Run::Alignment::MAFFT module?

Any help is much appreciated!

Best wishes,
Oliver