PAUP
I have stopped using PAUP* a long time ago. You could use MEGA 5-7 or Geneious to get pair-wise divergence (http://www.megasoftware.net/). Also, try these tools:
DnaSP http://www.ub.edu/dnasp/
trimAI http://trimal.cgenomics.org
Thanks a lot Dr. Ahmed.
Yes,MEGA 5-7 is a good alternate
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