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For most of the war the south did not have a commanding general, or general in chief of its armies. The Confederate President, Jefferson Davis, was a West Point graduate and a hero of the Mexican War, and was very active in the management of military affairs. The Confederacy was divided into "departments" geographically, with a general in command of each department, and also of all the forces located in his department. Thus, Robert E. Lee was in command of the Department of Northern Virginia, and also of the Army of Northern Virginia.

The popular perception is that Lee was in command of the southern armies throughout the war. In fact, Lee was eventually appointed as commanding general of the southern armies, but only for about the last two months of the war, by which time it was far too late to do any good. This was a change forced by the enemies of Jefferson Davis in the Confederate Congress.

The highest ranking Confederate general is someone nobody has heard of today, Samuel Cooper. Cooper had been Adjutant General of the US Army when Jefferson Davis was Secretary of War during the presidency of Franklin Pierce, and Davis hoped Cooper would help him run the Confederacy's armies when he nominated him to be first among the five four-star generals initially elevated by the Confederacy. Robert E. Lee was third on this list, behind Cooper and Albert Sidney Johnston. Johnston was killed at Shiloh in 1862, leaving Lee the second ranking Confederate general. Cooper spent the war as a glorified clerk in Richmond and never held a field command. Cooper was from New Jersey, but had married a Virginia girl and went south with her when the war started.

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Q: Who was the commanding officer of South during Civil war?
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