The code I posted doesn't even have 87 lines, so I'm not really sure what you expect me to do here.

Looking over the code I actually posted, there is a trivial syntax error on line 5. There is a stray and there. Removing this makes my code compile without error.

Maybe you can apply a similar technique to your code.

I delated "and" and I obtained

Global symbol "$index" requires explicit package name at /home/../scri
+pts/creaNexusMatrix.pl line 12.
Execution of /home/../scripts/creaNexusMatrix.pl aborted due to compil
+ation errors.
[download]

so I added

my $index;
[download]

and the code began;

my @column;
my $index;
my $curr_column = 0;
my $rows = 0;
while( @array) {
    if( $array[0] ne '--' ) {
        $column[ $curr_column ] ||= []; # a new column
        push @{ $column[ $curr_column ] }, shift @array;
        if( $rows < $#{ $column[ $curr_column ] } ) {
            $rows = $#{ $column[ $curr_column ] };
        };
    } else {
        $index++;
        shift @array;
    };
};

for my $row (0..$rows) {
    print join "\t", map { $_->[ $row ] } @column;
    print "\n";
};
[download]

Now the script works but I didn't obtain that I hope... I obtained:

--

0.0175

0.0483

0.0507

--

0.0471

0.0483

--

0.0287

--
[download]

Try

#!perl
use strict;

my @array = qw(
-- 0.0175 0.0483 0.0507
-- 0.0471 0.0483
-- 0.0287
--);

my @column;
my $curr_column = 0;
my $rows = 0;
while (@array) {
  if( $array[0] ne '--' ) {
    push @{ $column[ $curr_column ] }, shift @array;
    if( $rows < $#{ $column[ $curr_column ] } ) {
      $rows = $#{ $column[ $curr_column ] };
    };
  } else {
    $curr_column++;
    $column[ $curr_column] ||= [0]; # a new column
    shift @array;
  };
};

for my $row (0..$rows) {
  my @tmp = ();
  for (@column){
    if ( exists ($_->[ $row - $rows -1 ]) ){
      push @tmp,$_->[ $row - $rows - 1 ];
    }
  }
  print join "\t", @tmp;
  print "\n";
};
[download]

poj