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I can get a letter from a course instructor that I got a highest possible grade. He is a very well known professor at a top 5 institute. Of course, he can say little about my research.

I can also get a letter from my research collaborator who just got his PhD from a not-so-famous school. We worked on three papers so he can definitely comment my research in details. He is an assistant professor in a research-focused school rank at 100.

Which one is better for a research (PhD) program?

The program I am applying to requires two letters. The first letter is from a big name who I've done research with.

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    Why not both? . – Anonymous Physicist Dec 15 '19 at 7:43
  • @AnonymousPhysicist One slot left – dodo Dec 15 '19 at 23:33
  • Who got the other two slots? Balance is important... – cag51 Dec 16 '19 at 2:49
  • Also, what is the current job title of the recent PhD? Letters from post-docs or recent PhDs who have left academia carry ~no weight, in my experience. If he is already a professor, that's a different matter – cag51 Dec 16 '19 at 2:51
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Assuming you cannot submit both, I would go for the second one. You are applying to a research program and have research experience: the committee are going to be interested in that. If the committee is interested in your grades, they can already see them in your transcript.

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