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What makes Empathy unique from normal web browser chat is how it is integrated into your desktop.
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The messaging menu (mail icon) in the Notification Area can be used not only to launch Empathy, but also to open conversations. When a person says something and it is not "read", the messaging menu will list that conversation. For a few seconds after a contact comes online, their name will be listed in the menu to start a conversation. Either of these events will cause the messaging menu to turn green.
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The Me Menu, next to the shutdown icon can be used to set status. To do so, simply open it, then click Available, Busy, Away, Invisible, or Offline.
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When a contact comes online, or when someone says something, a notification will be shown in the top right corner of the screen. If you're not set to Available or are currently viewing the chat window, a notification will not show.