KnotGenom server enables to analyze entanglement of a single chromosome and links between chromosomes in the entire cell. All types of entanglement can be determined by different deterministic and probabilistic methods. The knotting complexity of the chromosome is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. Entanglement of links is also computed by Gaussian linking integral. Entangled chromosomes are presented graphically in an intuitive way. The stability of entanglement can be studied based on the relaxation method.