CoNTub is a software project written in Java which runs on Windows, Mac OS X, Linux and Unix Operating systems through any Java-enabled web browser. It is the first implementation of an algorithm for generating 3D structures of arbitrary carbon nanotube connections by means of the placement of non-hexagonal (pentagonal or heptagonal) rings, also referred as defects or disclinations. CoNTub generates the geometry of various types of nanotube junctions, i.e., nanotube heterojunctions and three-nanotube junctions, including also single-walled nanotubes (SWNTs) and multi-walled nanotubes (MWNTs).