The comparative index was introduced by J. Elyseeva (2007) as an efficient tool in matrix analysis, which has fundamental applications in the discrete oscillation theory. In this paper we implement the comparative index into the theory of continuous time linear Hamiltonian systems, study its properties, and apply it to obtain new Sturmian separation theorems as well as new and optimal estimates for left and right proper focal points of conjoined bases of these systems on bounded intervals. We derive our results for general possibly abnormal (or uncontrollable) linear Hamiltonian systems. The results turn out to be new even in the case of completely controllable systems. We also provide several examples, which illustrate our new theory.
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