You could just analyze it in isolation. I don't see any reason it's not just a 5 pin truss. Doesn't look like it takes any moment, so it doesn't need to be modeled together with the columns.
If you're using FEM, this will be a pain and a half to model with the whole structure. There are lots of things that could happen, like instability that's hard to track down and changing member sizes or dimensions for a lot of repetitive members. So I'd just model it as a beam with equivalent stiffness as the truss. And design the truss independently either in FEM or using hand calcs; it's nothing unusual.
Are you saying that these trusses are moment frames? Because I wouldn't design it that way. That's a whole can of worms. The building should have a lateral system. Another option, not great, is to design the columns as cantilevers from the foundation. If you must make the joists moment frames, you would have to design it together with the whole building and pay special attention to the moment transfer between the truss and the column, which I don't really advise.