convert file.gif -coalesce -layers OptimizeFrame newfile.gif

gistfile1.php

<?php 
$file_src = 'file.gif';

$im = new Imagick($file_src); 

$format = $im->getImageFormat();
if ($format != 'GIF') {
  // reject
}

$im = $im->coalesceImages(); // split file into individual images

foreach ($im as $frame) {
  $frame->optimizeImageLayers(); // optimize the image layers
}

$im = $im->deconstructImages();
$im->writeImages(newfile.gif, true);