foreach my $aref (@aoa) {
   printf("%-24s %7d %7d %f\n", @$aref);
}
[download]

If you search CPAN, I'm sure you'll find some module which automatically calculate how wide a column should be.

my @aoa = (
    [qw (GAL_up800.fasta  6  800  4.8)],
    [qw (hm01g.fasta  18  2008  36.144)],
    [qw (hm02r.fasta  9  1000  9)],
    [qw (train_muscle.fasta 7 50 0.35 )],
);

my $aref;   # Variable must be visible to the format

format STDOUT =
@<<<<<<<<<<<<<<<<<<<<<<  @<<<<<< @<<<<<< @<<<<<<
@$aref
.

foreach $aref (@aoa) {
    write;
}
[download]

For a more contemporary solution, why not try Perl6::Form? It looks very nice from what I've seen.

Caveat: Perl6::Form uses filters (by way of Perl6::Export) and requires Perl 5.8. Filters are generally seen as unfit for production code, and many people still use Perl 5.6.

It's certainly true that Perl6::Form only works with Perl 5.8 and later, so you can't use it if you're still on 5.6.

But I think your concern about source filtering is misplaced in this instance. Perl6::Form doesn't use a source filter on your code - it uses it on its own code. The problem with source filters that attempt to add syntax to Perl is that they will never parse the language completely accurately, and so will misbehave on certain code. (That's why Switch.pm is unreliable, for example.) In this case, the code that's being filtered is the source code of Perl6::Form, which obviously won't change, and has been verified to work with the Perl6::Export filter.

You might want to check out various table-generating modules. For example, I browsed a recent CPAN update to Text::TabularDisplay and it looks fairly nice. I'm sure there are others. That might be easier/nicer than messing with formats or other things.

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
[download]

#!/usr/bin/perl -w
use Text::Table;
my @aoa = (
    [qw (GAL_up800.fasta  6  800  4.8)],
    [qw (hm01g.fasta  18  2008  36.144)],
    [qw (hm02r.fasta  9  1000  9)],
    [qw (train_muscle.fasta 7 50 0.35 )],
);

my $tb = Text::Table->new();
$tb->load(@aoa);
print $tb;
[download]

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
[download]