What to list as affiliation when work spans multiple institutions? I began working on a paper during my undergraduate degree in the summer of 2014. I continued to work on the same paper into summer 2015, at which time I graduated and moved to a different university to pursue a graduate degree. However, all experiments failed and my collaborators and I were unable to produce any meaningful results. In fall 2015, while enrolled in graduate studies at the second university, I realized that the question at the centre of this paper could be answered using a completely different method. I contacted my collaborators and we have been able to produce some great results. 

Now I am writing the paper and wondering what I should list as my affiliation, since the project was begun at one university but overhauled and completed at another. I see four options: 


The old university
The new university
Both the old and new universities
The old university, with a “present address” note 


What is standard practice in a situation like this, where work is begun in one lab but completed in another? Does the re-design of the project from the second university complicate the issue?
Most journals understand that such complexities exist, and will allow you to list multiple institutions, so all four of your options are certainly viable.

That said, given that you have done much of your work on the paper while at your new institution, your new institution should certainly be listed as an affiliation, which means that you should be using either your option #2 (new only) or #3 (both institutions).

That leaves the question of whether the old institution should be listed or not.  From what I have seen, the customs on this tend to vary by field and also by institution: you can probably make a reasonable argument for either listing or not listing the old institution.  I would thus recommend talking with your co-authors to see what their feelings on the matter are, particularly if you have some co-authors from the old institution on the paper, who are the ones most likely to be upset if your judgement disagrees with theirs (in either direction).