Annoying Pop ups

Question

I am having annoying pop ups and new tab openings on safari on my Mac ( OSX 10.9). Also having small green boxes next to words on page that when I scroll over obviously show an ad.  Just started appearing in the last few days. When I cutoff Java Script they are gone but I cannot get through many sites without the Java Script

Answer 1

There is no need to download anything to solve this problem.
You may have installed one or more of the common types of ad-injection malware. Follow the instructions on this Apple Support page to remove it. It's been reported that some variants of the "VSearch" malware block access to the page. If that happens, start in safe mode by holding down the shift key at the startup chime, then try again.
Back up all data before making any changes.
One of the steps in the article is to remove malicious Safari extensions. Do the equivalent in the Chrome and Firefox browsers, if you use either of those. If Safari crashes on launch, skip that step and come back to it after you've done everything else.
If you don't find any of the files or extensions listed, or if removing them doesn't stop the ad injection, ask for further instructions.
Make sure you don't repeat the mistake that led you to install the malware. It may have come from an Internet cesspit such as "Softonic" or "CNET Download." Never visit either of those sites again. You might also have downloaded it from an ad in a page on some other site. The ad would probably have included a large green button labeled "Download" or "Download Now" in white letters. The button is designed to confuse people who intend to download something else on the same page. If you ever download a file that isn't obviously what you expected, delete it immediately.
Malware is also found on websites that traffic in pirated content such as video. If you, or anyone else who uses the computer, visit such sites and follow prompts to install software, you can expect more of the same, and worse, to follow. Never install any software that you downloaded from a bittorrent, or that was downloaded by someone else from an unknown source.
In the Security & Privacy pane of System Preferences, select the General tab. The radio button marked Anywhere  should not be selected. If it is, click the lock icon to unlock the settings, then select one of the other buttons. After that, don't ignore a warning that you are about to run or install an application from an unknown developer.
Still in System Preferences, open the App Store or Software Update pane and check the box marked
          Install system data files and security updates (OS X 10.10 or later)
or
          Download updates automatically (OS X 10.9 or earlier)
if it's not already checked.