Hi, supriyoch_2008,

• Please you may use strict in your script.
• Replace these lines in inv2.pl:

  ## Input the matrix text file: 
  print "\n\n Please type the filename(.txt) i.e. d1.txt: ";
   $DNAfilename = <STDIN>;
   chomp $DNAfilename;         
  ## To remove white space:
  $DNAfilename=~ s/\s//gis;
  # open the file, or exit
   unless ( open(DNAFILE, $DNAfilename) ) {
   print "Cannot open file \"$DNAfilename\"\n\n";
   exit;
   } # Line 10
   @a = <DNAFILE>;
  @m2=@a;
  [download]

  with these:

  my @m2;
  ## Input the matrix text file:
  print "\n\n Please type the filename(.txt) i.e. d1.txt: ";
  chomp( my $filename = <STDIN> );
  
  open my $fh, '<', $filename or die "can't open file $!";
  while (<$fh>) {
      push @m2, [ split /,/, $_ ];
  }
  close $fh or die "can't close file: $!";
  [download]

Note:
Ofcourse, your script(s) can be improved upon, but these should give you what you want to start with.
Hope it helps.