if you want to use Bioperl, here's an option. I couldn't find a module that would do this automatically, but I bet there is one out there. 
use strict;
use Bio::Seq;

my $dna = 'accatgagctgtacgtagcatctgagcgcgcatgactgtgactgacgtaggcagca';
my $seq = Bio::Seq->new( -seq => $dna);
my $end =  $seq->length -10;

my @windows;
for(my $i= 1; $i < $end; $i+=2) #increase by one codon each time.
  {
    push @windows, $seq->subseq($i, $i+9);
  }
print join "\n", @windows;

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In reply to Re: substr help by geekgrrl
in thread substr help by Anonymous Monk

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