Doxy can treat a number of co-infections. However, everyone is different and it is not a guarantee. It is not really adequate by itself to treat Bartonella or Babesia, which are common co-infections.
Buhner has various herbal protocols for co-infections. He has updated protocols in his books. His books are pretty reasonably priced. You can check out his website to get an idea though. The website is no longer updated or maintained.
There are other herbal protocols, such as Cowden. Buhner is very popular. I find a combination of antibiotics and herbals is best for me.
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a particular her by doing a search in the upper right hand Search Bar. Or you can ask questions.
It is good to see an ILADS trained Lyme Literate doctor who can diagnose you based on symptoms. Then, you will know what to target and what meds to focus on. The "New to Lyme" thread has lots of great info, including symptoms lists for different infections. I have found it very helpful. There is also a lot of great info on detoxing.
Here's Buhner's site:
http://buhnerhealinglyme.com/the-protocols/