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I'd like to have mutt sort messages newest first, and have threads displayed with the newest message at the top of the thread. Right now I have the message list in the correct order, but the sub-sorting within threads is backwards (newest at bottom of thread). Here's my current configuration...

set sort = threads
set sort_aux = reverse-last-date-received

Is there any option to control sorting within threads?

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If I understand you correctly, you're reversed the sorting of threads but you meant to reverse the sorting within threads, so swap them:

set sort=reverse-threads
set sort_aux=date-received

I think Mutt always displays the thread title on the oldest message in the thread, even when it ends up sorted at the bottom.

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