The suggestion of converting a gif to a png to retain transparency was useful. However the steps used to maintain the transparency work for a gif as well, so the conversion step is not necessary. Just do everything the same, and save as a gif anyway. i.e.
<?php
$g_iw is new image width
$g_ih is new image height
$img_src=imagecreatefromgif($g_srcfile);
$img_dst=imagecreatetruecolor($g_iw,$g_ih);
imagecolortransparent($img_dst, imagecolorallocate($img_dst, 0, 0, 0));
imagealphablending($img_dst, false);
imagesavealpha($img_dst, true);
imagecopyresampled($img_dst, $img_src, 0, 0, 0, 0, $g_iw, $g_ih, $g_is[0], $g_is[1]);
imagegif($img_dst, $g_dstfile);
imagedestroy($img_dst);
?>
