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I will be applying to PhD science program in the US.

I want to avoid taking recommendation letter from my bachelor thesis co-supervisor since he might not give me the best recommendation entirely due to reasons other than work.

To compensate, I will have a very strong recommendation from the head supervisor who guided my bachelor thesis, who can write about my contribution to the same thesis project.

In this circumstance, will it look suspicious from the application point of view, if I do not have the recommendation from my co-supervisor ?

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It looks totally normal to hand in the letter from the main supervisor instead of the co-supervisor. If you need a second letter, ask someone from another project. I would not advise to hand in two letters from the same project anyway, it looks as if you have nothing else to offer.

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