i could use the following factory instead of that in the 1st script,but that would give me a file(out_file)

my $factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix => 'BLOSUM','outfile' => 'out_file','outype'=clustalw);

This file matches to first line my $alnio = Bio::AlignIO->new('-file'=> 'out_file','-format' => 'clustalw');

of the 2nd script,and when combining the two scripts, the whole (1+2) script works fine. But

yeap, i want to pass a variable and have only one file produced at the end of final whole (1+2)script with my final Tree.

In reply to Re^2: how to combine these two scripts in perl? by dimitris852
in thread how to combine these two scripts in perl? by dimitris852

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