Our modern weapon systems are the result of thousand of years of arms race, where one system was invented to counter another (usually earlier) system. E.g. Bombers -> AAA/SAMs/Interceptors -> Ballistic/Cruise missiles -> Anti-missile defense... and so on. Basically, all our weapons originated from the fundamental purpose of killing/maiming human beings.
It is extremely unlikely that any alien weapon system would have followed a similar development path to ours, unless they have been observing our civilization for some time. Also remember alien biology will be very different from ours.
If we assume that the aliens have just chanced upon the Earth, I think we'll find that their weapons are thoroughly unsuitable against us humans. Of course, our weapons will probably be equally ineffective against them. Ironically, the more technologically advanced the weapon system, the more specialized it becomes, so probably less useful. There is not going to be dogfights with F-18s, or hacking into computer systems.
So both sides may have to start inventing new weapons from scratch.
Sorry but that is not exactly correct. A gun is a gun is a gun, a spear is a spear is a spear and a knife is a knife is a knife. They will punch a hole or cut a wound no matter what. All these weapons actually originated or adapted mainly to kill other species (animals) before Man. Well, a gun is first made to kill other people but it also went and killed animals.
Every weapon will kill other living things no matter what. Poisons for example are universal. Its as toxic to Man as it with insects.