Your bug is caused by serious scoping problems. Because you are not using any scoping or lexical variables. The $i in your outer look is the same variable as the $i in your subroutine.
As long as $leg is greater than $number_of_sequences (and if it is generated using $min_length, it will be), the loop will terminate after one call.
You probably wanted: 


$number_of_sequences=12;
$max_length=50;
$min_length=30;

my @set;
for (my $i=0; $i < $number_of_sequences;$i++) {
   my $aminoseq = genseq($aminoseq);
   print "$aminoseq\n\n";
   push (@set,$aminoseq);
}


sub genseq {

  my $leg=randomlength();
  my $seq;
  for (my $i=0; $i<$leg; $i++) {
    $seq.=randomaminoacid();
  }
return $seq;
}

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use strict would have caught this and many other problems in your code. Incidently, if the three variables at the top of your code are constant, if would declare them as: 
use const NUMBER_OF_SEQUENCES => 12;
use const MAX_LENGTH => 50;
use const MIN_LENGTH => 30;

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That way it is clear that they are constants, and it is impossible to inadvertently change them.
Read the Camel book for more information on scoping and lexical variables.
Hope this helps,

-pete
"Pain heals. Chicks dig scars. Glory lasts forever."

In reply to Re: Running a subroutine a certain number of times by dreadpiratepeter
in thread Running a subroutine a certain number of times by Anonymous Monk

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