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medschoolwoo

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Yes, your calculated GPA on your application will use all the classes you have taken at any institution. For rec letters I would use the GPA that will appear on your application, meaning the "new overall GPA", but unless it really changes your GPA I don't think it matters much for rec letters. You will need to send transcripts into AMCAS/ACCOMAS for every institution you attended.
 
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You must provide AMCAS with every transcript from every post-secondary school you have attended (including dual enrollment).

Rec letters need not include your GPA and the opinion of your letter writers on your GPA is not what we are looking for from the letter writers. We want, instead, the letter writer's personal assessment based on their personal observations of your academic performance, deportment, involvement on lab, and in activities that the writer observed.

AMCAS has a handout for letter writers that you might want to include along with your request for a LOR.
 
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