In Bhutan, clapping is done to ward off evil spirits and not as a welcome gesture.
The gathering, which included Bhutanese Prime Minister Tshering Tobgay and members of the National Assembly and the National Council, broke into an applause as Modi ended his address to the joint session.
The joint sessions are held in the chamber of the National Assembly (lower house), attended by members from the National Council (upper house).
There were interpreters at hand to translate his speech in which he shared his thoughts on India-Bhutan relations.
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Describing the Himalayas as a shared legacy, Modi stressed on the need to develop the ecology of region and said India is planning to open a university for Himalayan studies.
Modi said people believe that Himalayas divide but he was of the view that the Himalayas actually unite.
At the joint session, the ministers of the Bhutan government were seen wearing an orange robe over their traditional dress, the MPs, 47 from the National Assembly and 25 from the National Council -- were wearing blue robes.