Tools for comparing/visualizing FASTAs? I have two FASTAs/assemblies of the same species, but the bases are somewhat different. I would like to explore this. 

What tools/methods exist to compare two FASTAs and see the difference in structure between them? Are there visualization tools available, something like IGV? 

I think users would need to do a multiple-sequence alignment between these FASTAs, and then check for the differences between them. However, I don't know if a "standard approach" exists to do this.
You can try Mauve multiple genome aligner.