use strict;
use warnings;

while (<DATA>) {
    s/a/x/g unless $. & 1;
    print;
}

__DATA__
Anyone know a way to apply a
substitution in a file to every
other line rather
than the hole file?

##</code><code>##

Anyone know a way to apply a
substitution in x file to every
other line rather
thxn the hole file?