Help with adding partitions and a guidetree for raxml inference

[Diego Soto Arancibia]

Hi everyone! I'm trying to become independent from CIPRES haha and give it a try to the manual method for raxml, through Ubuntu (inside Windows WSL) . I managed to run a pipeline to generate a tree from a concatenated matrix of five plant species genes, but i don't know how to add the partitions. How can this be done? Also, is it possible to add a guide tree generated by phylomaker to correct some of the topologies of the tree generated by raxml? 

Thank you all in advance!