I'm currently pursuing an MS with the intent to apply to PhD programs this fall. I intended to switch from MS to PhD at my current institution, but my advisor and I don't really get along well. There's a whole lot of history behind it, but I'll skip it to be concise (unless you all really want to know!). Plus, I have issues with the quality of
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Personally, I would ask for the letter from your advisor, and go with whoever you think will give you the best for your rest, regardless of how they're connected to you.
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I was in a similar position when I was working as a research assistant after undergrad and applying to PhD programs. My boss and I didn't have a good relationship, but he ended up volunteering to write me a letter when he found out I was applying, and it can't have been too bad, since I was accepted to most schools I applied to.
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I also agree with the others as well, if you don't include at least one LOR from your masters program it will draw some probably negative attention to your application. Also, it's a small world and if you're keeping within the same field or research interest, the programs/professors you're applying to might have either heard of you or know your mentor.
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