There is no single correct answer for that question. It depends a lot on the diversity of sequences in your ingroup, and how far distant the outgroup is from the ingroup. In my opinion, if the outgroup is so far distant from the ingroup that the model of evolution or the partitions would be altered significantly by including it, you should be using a different outgroup or perhaps using midpoint rooting with no outrgroup. Running ModelTest or a modeltest version within PartitionFinder should not take too long, so you should be able to run it both with and without the outgroup to see if there is any change.

https://www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html

http://evomics.org/learning/phylogenetics/jmodeltest/

http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_Modeltest_Lab

http://www.robertlanfear.com/partitionfinder/

http://www.robertlanfear.com/partitionfinder/assets/Manual_v2.1.x.pdf

There is no single correct answer for that question. It depends a lot on the diversity of sequences in your ingroup, and how far distant the outgroup is from the ingroup. In my opinion, if the outgroup is so far distant from the ingroup that the model of evolution or the partitions would be altered significantly by including it, you should be using a different outgroup or perhaps using midpoint rooting with no outrgroup. Running ModelTest or a modeltest version within PartitionFinder should not take too long, so you should be able to run it both with and without the outgroup to see if there is any change.

https://www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html

http://evomics.org/learning/phylogenetics/jmodeltest/

http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_Modeltest_Lab

http://www.robertlanfear.com/partitionfinder/

http://www.robertlanfear.com/partitionfinder/assets/Manual_v2.1.x.pdf

Dear Brian Thomas Foley ,

thank you for your answer.

It seems that it is better to include the outgroup in all analyses then. Dr. Rob Lanfear also suggested me to proceed this way.

Thank you,

Best,

Manolo