twhirl marks tweets, replies and direct messages in your timeline as new or unread when it receives them, by adding a small dot in the top right corner. Simply click somewhere inside the tweet to mark it as seen. Pressing the dash or minus key “-” or clicking the small button below the timeline will mark all tweets as seen.

Unfortunately, the twitter servers do not support marking tweets as seen, so if twhirl fetches old tweets, replies or DMs on startup, it will mark them as new again, even if you marked them as seen in a previous session.