How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree

Question

[pragati.bhingare]

Hello,

I apologise for very basic question but I am very new to biology and have very specific knowledge of this field.

I am currently working on Bioinformatics in my machine learning project which is why I need to be sure about obtained results before I proceed. I am not aware of all the tools used in genomics/bioinformatics.

I would like to know that what tools can be used if I want to trace and observe the strand orientations in the ancestral inversion mutations?

I would like to know the key concepts as well, using which I can automate the process in my program and display the orientation. Thank you in advance.