For a jquery way, you could use this function which iterates through the rows in your table, checking the visbility of the row and (re)setting a class for visible odd rows.
function updateStriping(jquerySelector) {
var count = 0;
$(jquerySelector).each(function (index, row) {
$(row).removeClass('odd');
if ($(row).is(":visible")) {
if (count % 2 == 1) { //odd row
$(row).addClass('odd');
}
count++;
}
});
}
Use css to set a background for odd rows.
#mytable tr.odd { background: rgba(0,0,0,.1); }
Then you can call this zebra-striper whenever by using:
updateStriping("#mytable tr");