In the current world, Botnets are widely spreading with a really great pace. In such situations, it is quite hard to keep up with the bad guys. This means that we need something that is proactive, than solutions that are reactive. BotHunter is a proactive tool that helps protect networks of computers from getting compromised due to botnets.
You can download or visit BotHunter from its original site: http://www.bothunter.net. This is how it looks:

About BotHunter [To read more, check out the Source: About]:
Regardless of how malware enters your network (through innocent web surfing, email attachments, direct exploit, or by attaching your laptop to the wrong wireless network), once a machine within your perimeter is compromised your whole network is under threat. BotHunter helps you quickly identify and isolate these infected machines, and helps you figure out who really owns your computers.
What is BotHunter
BotHunter is NOT an intrusion detection system, firewall, spam blocker, or antivirus tool. These tools generally don’t work in helping you rid your network of malware infections. Rather, BotHunter takes a different approach. It is an entirely new network defense algorithm designed to help everyone from network administrators to individual Internet-connected PC users detect whether their systems are running coordination-centric malware (such as botnets, spambots, spyware, Trojan exfiltrators, worms, adware). It is based on an algorithm called network dialog correlation, developed under the Cyber-TA research program (http://www.cyber-ta.org), by the Computer Science Laboratory at SRI International.
BotHunter monitors the two-way communication flows between hosts within your internal network and the Internet. It aggressively classifies data exchanges that cross your network boundary as potential dialog steps in the life cycle of an ongoing malware infection. BotHunter employs Snort as a dialog event generation engine, and Snort is heavily modified and customized to conduct this dialog classification process. Dialog events are then fed directly into a separate dialog correlation engine, where BotHunter maps each host’s dialog production patterns against an abstract malware infection lifecycle model. When enough evidence is acquired to declare a host infected, BotHunter produces an infection profile to summarize all evidence it has gathered regarding the infection. In short, BotHunter helps you rapidly identify infected machines inside your network that are clearly and helplessly under the control of external malicious hackers.
Dialog correlation attempts to produce classification events for certain network traffic exchanges that are produced and received by your computers. While not all network traffic exchanges produce a dialog event, those that do contribute to an evidence trail that may lead to a malware infection diagnosis report for the associated computer. Dialog events are fed directly into a separate dialog correlation engine, where each host’s individual dialog production pattern is mapped and scored against an abstract malware infection life cycle model. When the dialog correlation algorithm determines that a host’s dialog production patterns maps sufficiently close to the life cycle mode, the host is declared infected, and an infection profile is generated to summarize all evidence regarding the infection. See our Samples Page, for examples of infection profiles produced from a wide variety of Internet malware.
BotHunter is funded through the Cyber-Threat Analytics research grant from the U.S. Army Research Office, and is free to all end users to help you combat malware infections. In addition, BotHunter includes an auto-update service that allows fielded systems to receive the latest threat intelligence regarding new sources for ad and spyware management, botnet control sites, backdoor and control ports, and malware-related domain name lookups. The update service also publishes new dialog analysis rules to help BotHunter recognize emerging exploits and malware communication patterns. Modern malware defenses need to be adaptive and aware of the latest strategies used by Internet malware, and BotHunter is ready to meet this challenge.
This project is being run by SRI International, which is an independent, nonprofit research institute conducting client-sponsored research and development for government agencies, commercial businesses, foundations, and other organizations. SRI also brings its innovations to the marketplace by licensing its intellectual property and creating new ventures. [Source: SRI]
SRI collects all the malware research data, analyzes them and displays them in their Malware Threat Center, a snapshot of which is pasted below:

SRI International has been doing great research with any malware in existence, especially the famous ones out there. They have been publishing great research from time-to-time. BotHunter’s UserGuide and GUIGuide are available Online. In their ‘Coming Soon‘ section of the website:
Here is a summary of what we are working on
o BotHunter v2.0 is under development. This version will introduce an entirely new user interface experience and will
support large-scale remote management. This version will take Bot hunting to a whole new level.
o Our research team anticipates forthcoming announcements on entirely new technologies to combat malware.
Thanks for your support!
The BotHunter’s Community Respository, is an open list of Botnet C&C IPs, location details[City, Region and Country], Domain/NetSpeed Servicer Provider, Forensics and Evindence Summary: Performed by the Botclient Victim. This is great stuff for people performing research and trying to shut down botnets out there. We hope that this blog post helped you to learn more about BotHunter. Thank you for choosing our blog!