my @content = (); close(FH); my $no_of_seq = scalar(@content); my @myArray; foreach my $row (@content) { my @columns = split(/\s+/,$row); push(@myArray,\@columns); # print "@columns"; } for($row = 0; $row < $no_of_seq; $row++){ for($col = 0; $col < $no_of_seq; $col++){ print($myArray[$row][$col], "\t"); } print("\n"); }