When do you consider author order? This can be a difficult topic for new investigators and can very much depend on the department you work in. In my experience, it is always best to have a discussion about author order early on, this of course isn't to say things can't be changed later on, but at least you know where you stand.
There is a nifty, little program that can help determine order call Authorder. While there are nuisances to choosing the order that this program won't pick up, it might help you to make an argument about order when you feel that perhaps your contribution to the work isn't being given enough weight.
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