While SpamAssassin comes with a set of predefined rules, Bogofilter needs to be taught first before it will automatically filter junk mail. If you only train Bogofilter on bad messages, it will assume all mail is bad (because it does not know any difference) hence it will not make any decisions until the database is sufficiently large to determine what is and is not spam. In any case, when you first start using junk mail blocking, check the Junk mail folder frequently to be sure that legitimate mail doesn't get flagged as junk mail.
If Evolution misses junk mail, right-click the message, then click Mark as Junk, or mark the message and press Ctrl+J or click the Junk button in the tool bar. When you correct it, the filter can recognize similar messages in the future, and becomes more accurate as time goes on.
If legitimate mail is incorrectly flagged, remove it from the Junk folder by right-clicking it and selecting Mark as Not Junk or pressing Shift+Ctrl+J, or mark the message and click the Not Junk button.
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