How are these frequencies determined? Has any effective research been done on using lights ( shades of green and yellow ) for healing? 

From page 136 of the February 2016 User's Guide:

Database: Spooky2's main database is made up of 10 sub-databases.

‣ PROV has produced consistent results in virtually all subjects it was used with.
‣ BIO and VEGA are both excellent, based on Russian frequency research.
‣ CAFL is the Consolidated Annotated Frequency List, amassed from the experience of Rife experimenters over years.
‣ XTRA is a collection of sets from various sources, all chosen for their reputation for effectiveness.
‣ CUST is your own personal database.
‣ RIFE is a collection of Dr. Royal Raymond Rife's original frequencies.
‣ HC is Dr. Hulda Clark's database. Use with a square wave, 100% positive Offset, and Amplitude of 9.5.
‣ KHZ is a collection of higher frequencies. Use with a square or inverse sawtooth wave, 100% positive Offset, and Amplitude of 9.5.
‣ ALT consists of sets based on Ayurvedic knowledge and practise, solfeggios, and planetary frequencies.

You may download the User's Guide from here:
http://spooky2.com/downloadsPage/index.html

As to color therapy, please check this out:
http://www.dinshahcolortherapy.com/

I have used the colored gels and they worked well for me. You will need to buy the colored gels and the Dinsha color therapy book where application guide/use is found.

Please check the blog:
Rife Frequency Sources
http://www.spooky2-mall.com/blog/rife-frequency-sources/

For more details, please check the link:
http://www.spooky2.com/forums/viewtopic.php?style=1&f=5&t=4714