TCP analysis tool: 
The purpose of the tool is to provide more complete and accurate results for identifying and characterizing out-of-sequence segments than those provided by prior tools such as tcpanaly, tcpflows, LEAST, and Mystery. Our methodology classifies each segment that appears out-of-sequence (OOS) in a packet trace into one of the following categories: network reordering or TCP retransmission triggered by one of timeout, duplicate ACKs, partial ACKs, selective ACKs, or implicit recovery. Further, each retransmission is also assessed for whether it was needed or not.

Code: The documentation for using the tool and the tool itself is located here.

Tbit (TCP Behavior Inference Tool):
Tbit is an excellent tool for inferring TCP behavior and hence could be used to understand the behavior of different implementations. It can be used to create different scenarios to study TCP behaviors under different circumstances. The original tool is available here. I have modified the tool to test for different scenarios. Details for this tool will be available online soon.

Code: Tbit modifications done by me are available here.

EON (Testing Efficacy of Overlay Routing):
We emulate an overlay network by gathering ping data from a collection of nodes in a real wide-area network and then sub-sampling the data as appropriate to emulate an overlay network with the desired degree of logical connectivity between nodes. Each node in the network runs two programs: a "ping" module that emulates the probing mechanism in an overlay and a "state exchange" module that emulates mechanism used to propagate measurement data to other nodes. The tool for collecting the ping data was designed by modifying the RON code.

Code: The tool I used to collect the ping data in an automated manner is available here. The scripts used to analyze the data are available here.

SOLIX (Secure OnLine Information eXchange):
SOLIX was developed for VJTI (undergraduate college) to provided secure transmission of information over a local network. Core of project is a security package, providing symmetric (RSA) and asymmetric (AES) key encryption. Around it is developed a messaging service with several features including File Transfer, Data Compression, and offline messages.

Code: Code for this tool is not available publicly. I will try and make parts of it available soon.