The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints.
SiLiX is now incorporated in hundreds of projects in the world (in particular in France) and is widely cited.
SiLiX adopts a graph-theoretical framework to interpret similarity pairs as edges of a network. A very efficient algorithm, based on the Disjoint Sets Data Structure, allows the computation of sequence families with low time and space requirements.
A parallel version of SiLiX, based on MPI, is also available in this package and has been proved to be scalable, so that its allows the study of very large datasets.
SiLiX is already included in the analysis pipeline for HOGENOM.