Methods and systems for automated generation of malicious traffic signatures, for use in Intrusion Detection Systems (IDS). A rule generation system formulates IDS rules based on traffic analysis results obtained from a network investigation system. The rule generation system then automatically configures the IDS to apply the rules. An analysis process in the network investigation system comprises one or more metadata filters that are indicative of malicious traffic. An operator of the rule generation system is provided with a user interface that is capable of displaying the network traffic filtered in accordance with such filters.