If you remove unused code and variables and use more idiomatic perl you get something like:

#!/usr/bin/perl
use strict;
use warnings;

use SDL::App;
use SDL::OpenGL;


$| = 1;

my %conf = (
    title  => 'Game',
    width  => 1200,
    height => 900,
    fovy   => 125,
    );

my $sdl_app = SDL::App->new(
    -title  => $conf{ title },
    -width  => $conf{ width },
    -height => $conf{ height },
    -gl     => 1,
    );

SDL::ShowCursor( 0 );

my %rule = (
    n => 'nlnrrnln',
    l => 'lnrnrnlln',
    L => 'LnnRnnL',
    r => 'rnllnrrn',
    R => 'RnnLnnR',
    );
my %rule2 = (
    n =>    0,
    l =>   60,
    L =>  120,
    r =>  -60,
    R => -120,
    F =>    0,
    );

for ( 1 .. 4 ) {
    glClear( GL_COLOR_BUFFER_BIT );
    glMatrixMode( GL_PROJECTION );
    glLoadIdentity;
    my $aspect = $conf{ width } / $conf{ height };
    gluPerspective( $conf{ fovy }, $aspect, 1, 1000 );
    glMatrixMode( GL_MODELVIEW );
    glLoadIdentity;
    # Move the viewpoint so we can see the origin
    glTranslate( 0, -2, -10 );
    my @pos = ( 0, 0, 0 );
    my $rot;
    for my $char ( split //, iterate( 'nLnLnL', 4, %rule ) ) {
        $rot += .01745 * $rule2{ $char };
        my ( $x, $y ) = $char eq 'n' ? ( cos( $rot ), sin( $rot ) ) : 
+( 0, 0 );
        @pos = ( $pos[ 0 ] + $x, $pos[ 1 ] + $y, 0 );
        for my $step ( 0 .. 9 ) {
            draw_cube( [ $pos[ 0 ] - ( $x / 10 * $step ), $pos[ 1 ] - 
+( $y / 10 * $step ), $pos[ 2 ] ], .03, ( .2, .2, .2 ) );
            }
        }
    print '.';
    sleep 1;
    $sdl_app->sync;
    }

print "\nDone.\n"


sub iterate {
    my ( $inp, $iterations ) = @_;
    my %rules = @_;
    for ( 1 .. $iterations ) {
        $inp .= join '', @rules{ split //, $inp };
        }
    return $inp;
    }

my @indices = qw(
    4 5 6 7
    1 2 6 5
    0 1 5 4
    0 3 2 1
    0 4 7 3
    2 3 7 6
    );
sub draw_cube {
    # A simple cube
    my ( $x, $y, $z ) = @{ $_[ 0 ] };
    my $s = $_[ 1 ];
    glColor( @_[ 0, 1, 2 ] );
    glBegin( GL_QUADS );
    my @vertices = (
        [ -$s + $x, -$s + $y, -$s + $z ],
        [  $s + $x, -$s + $y, -$s + $z ],
        [  $s + $x,  $s + $y, -$s + $z ],
        [ -$s + $x,  $s + $y, -$s + $z ],
        [ -$s + $x, -$s + $y,  $s + $z ],
        [  $s + $x, -$s + $y,  $s + $z ],
        [  $s + $x,  $s + $y,  $s + $z ],
        [ -$s + $x,  $s + $y,  $s + $z ],
        );
    for my $face ( 0 .. 5 ) {
        for my $vertex ( 0 .. 3 ) {
            glVertex( @{ $vertices[ $indices[ 4 * $face + $vertex ] ] 
+} );
            }
        }
    glEnd();
    }
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