Is there any programming libraries available that will parse an HTML document, execute JavaScript and then allow me to navigate the DOM? This needs to be performed server s
PhantomJS does this and can be used with any server side language. See some integration modules below for NodeJS and PHP
NodeJS
https://npmjs.org/package/node-phantom
https://github.com/sgentle/phantomjs-node
PHP
https://github.com/diggin/php-PhantomjsRunner