"Where is the tree?"
Translation:Onde está a árvore?
I can't really explain why, but I think that "Onde é a árvore?" is a weird question in portuguese. I'm brazilian. Maybe you should go with "Onde fica a árvore?", if está is strange for you ;)
Now that I thought about it, I think there's an explanation of why we don't use É as much as Está for this type of sentence. A tree is not a place, it's a thing. If you are going to ask "Where is that place?" then asking "Onde é aquele lugar?" makes sense, but with things (imagine here that a tree is an object) Está suits better.
Two people go to forest and one asks: "onde é a árvore a qual você me falou?"
Yes, I know that you can use it. It just sounded weird to me. And when I read that sentence the first thing that passed through my mind was "Onde está a árvore?". It's really a matter of context.