mdendro is an R package that provides a comprehensive collection of linkage methods for agglomerative hierarchical clustering on a matrix of proximity data (distances or similarities), returning a multifurcated dendrogram or multidendrogram. Multidendrograms can group more than two clusters at the same time, solving the nonuniqueness problem that arises when there are ties in the data. This problem causes that different binary dendrograms are possible depending both on the order of the input data and on the criterion used to break ties. Weighted and unweighted versions of the most common linkage methods are included in the package, which also implements two parametric linkage methods. In addition, package mdendro provides five descriptive measures to analyze the resulting dendrograms: cophenetic correlation coefficient, space distortion ratio, agglomerative coefficient, chaining coefficient and tree balance.

MultiDendrograms is a program to make the Hierarchical Clustering of real data.
It implements variable-group algorithms to solve the non-uniqueness problem found in the standard pair-group algorithms and implementations.The standard approach consists in choosing a pair, breaking the ties between distances, and proceeds in the same way until the final hierarchical classification is obtained. However, different clusterings are possible depending on the criterion used to break the ties (usually a pair is just chosen at random!).

MuxViz is a framework for the multilayer analysis and visualization of networks. It allows an interactive visualization and exploration of multilayer networks, i.e., graphs where nodes exhibit multiple relationships simultaneously. It is suitable for the analysis of social networks exhibiting relationships of different type (e.g., family, work, etc) or interactions on different platforms (Twitter, Facebook, etc), biological networks characterized by different type of interactions (e.g., electric, chemical, etc, or allelic, non-allelic, etc), transportation networks consisting of different means of transport (e.g., trains, bus, etc), to cite just some of the possible applications.