MEGA? PAUP*? I don't know what the kids are using these days.

Try Clustal  (many versions)

good luck

Are each of these fasta files aligned? Once they are aligned you can then concatenate them into a single matrix. I quite like SequenceMatrix for a drag-n-drop GUI and seeing the distances between each component of the supermatrix, and it outputs in a few different formats. For command-line concatenation I would suggest FASconCAT, a nicely made perl utility which can then be part of a pipeline, if you are working in that kind of environment.

http://gaurav.github.io/taxondna/

https://www.zfmk.de/en/research/research-centres-and-groups/fasconcat-g

Thank you Alastair R Tanner ! I liked SequenceMatrix ! pretty user friendly!

Thank you Mustafa Faddagh and Nathan Bendik! I have worked with the softwares! thanks anyway!