Which organic compounds would be the best to analyze in order to determine if two species are closely related?

Amino acids or the proteins of the cell

DNA code is transffered to mRNA in the nucleus through a process called
transcription. 

Nucleus, the control center of the cell is the organelle which intiates, enables, and manages the various simplex. compound and complex cellular activities. It also stores the DNA of the cell which is then replicated and recopied over a hundredth and thousandth times over through cell division processes. In the nucleoplasm -nucleolus, the inner part of nucleus of a cell is where the DNA to mRNA and to protein; vice-versa happens.