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But the Afghan seat at the United Nations continues to be held by former President Burhanuddin Rabbani.
BBC: Analysis: Who are the Taleban?
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Mr Masoud was defence minister in that government, headed by Burhanuddin Rabbani, which, theoretically, is still in existence in exile.
ECONOMIST: Ahmad Shah Masoud
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But Burhanuddin Rabbani, the Alliance's leader and self-styled president of Afghanistan, was sidelined, apparently under pressure from the American and German governments, among others.
ECONOMIST: An outline for power-sharing that may just work. Maybe
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Burhanuddin Rabbani was killed at his home in Kabul on 20 September when meeting a man who said he was carrying an important peace message from the Taliban.
BBC: Haqqani network denies killing Afghan envoy Rabbani
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He himself was injured in 2011, when the man in charge of peace talks - the former Afghan President Burhanuddin Rabbani - was killed by a suicide bomber disguised as a Taliban peace envoy.
BBC: Afghanistan eyes Taliban peace ahead of Nato withdrawal
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Efforts to hold talks have been hit by a string of setbacks, including the assassination in September of Burhanuddin Rabbani, the head of the peace council, which had been liaising with the militant group.
BBC: Afghan Taliban back Western proposal for Qatar office
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But he warned that insurgents were changing tactics to focus on high profile targets such as August's raid on the British Council offices in Kabul and the recent assassination of the country's former president Burhanuddin Rabbani, which he described as a "major setback".
BBC: Philip Hammond: Afghanistan progress not 'irreversible'