The following will do what you want. Just change the call to printspaced() so it passes whatever delimiter you want as the first argument.

use strict;
use warnings;

chomp (my @data = <DATA>);
$_ = [split / /] for @data;

printspaced('  ', \@data);

sub printspaced {
    my ($s, $d, @f, $f) = @_;
    push @f, '%-'.$_.'s' for widths($d);
    $f = join($s, @f)."\n";
    printf($f, @$_) for @$d;
}

sub widths {
    my ($d, @r, $i) = $_[0];
    for (@$d) {
        no warnings;
        for ($i = 0; $i <= $#$_; $i++) {
            $r[$i] = length($_->[$i]) if length($_->[$i]) > $r[$i];
        }
    }
    return @r;
}

__DATA__
GAL_up800.fasta 6 800 4.8
hm01g.fasta 18 2008 36.144
hm02r.fasta 9 1000 9
train_muscle.fasta 7 50 0.35
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