Thuja is the best all-round remedy for after-effects or side-effects of (traditional) vaccinations, but it`s not the only important homeopathic remedy. Thuja is indicated if your companion is off colour with possibly vomiting, diarrhoea and sudden skin upsets. If this is the case then give Thuja 30c (or 30K) 3 times daily for a week approx. (i.e. 5-10 days) as necessary.
Depending on the presenting symptoms a different remedy may be indicated. For example Sulphur 6c or 30C if it`s necessary to boost the dog`s natural defence system and the dog is obviously off colour, dull, generally listless and possibly off its food after vaccination, etc.
Nux vomica 6c or 30 c (or 6k or 30k) is used after vaccination to eliminate toxins from the body and is indicated if there are digestive upsets causing vomiting and diarhoea, etc.
Unfortunately it`s too much to explain it all in a short post.