General David Petraeus was to step down from his post as the top US commander in Afghanistan on Monday, after a week in which two of Afghan President Hamid Karzai's closest allies were assassinated. Petraeus, who served as commander of the US-led international force for one year, has claimed some progress against the Taliban with NATO-led troops stabilising parts of the south as Afghan security forces prepare to take over. The general is leaving to take charge of the CIA and a change of command ceremony is scheduled for Monday morning to hand control of the mission to Lieutenant Colonel David Rodriguez. Chairman of the US Joint Chiefs of Staff Admiral Mike Mullen, who is visiting the country and met with Karzai on Sunday, was also expected to attend the ceremony. The Petraeus legacy in Afghanistan remains in question as violence continues to rage, underscored by the shock killings of two of Karzai's top allies in the south -- his brother last Tuesday and a senior adviser on Sunday. Armed attackers murdered senior adviser Jan Mohammad Khan, the former governor of southern Uruzgan province, in a raid on his Kabul home on Sunday, agovernment and police officials told AFP. The assassination came just days after the president's half-brother Ahmed Wali Karzai was shot dead by his own head of security at his home in the southern province of Kandahar. The Taliban have claimed responsibility for both the killings. Just hours before Sunday's attack, a ceremony was held in central Bamyan province marking the start of a security transition from NATO to Afghan forces, a process that will see the departure of all foreign troops by 2014. Petraeus took charge in Afghanistan following his perceived success in turning around the Iraq war. He introduced a similar approach to counter-insurgency in Afghanistan, backed by a buildup of some 33,000 American troops, now due to go home by the end of 2012. Analysts have already warned that the killing of Wali Karzai may trigger a turf war for control of the critical southern heartland that could embolden the Taliban and reverse NATO gains. The deaths come at a critical juncture, just days after 3,000 Canadian troops ended their combat mission in Kandahar and in the same week that Washington began the troop drawdowns that are due to end in late 2014. The killings -- and a Taliban attack on the Intercontinental hotel in the heart of Kabul last month that left 21 dead -- have fuelled doubts about the readiness of Afghans to manage national security. After nearly 10 years of war, there are still around 150,000 foreign troops in Afghanistan, including nearly 100,000 from the United States.