Abstract Motivation Previously, we developed a computational model to identify genomic co-occurrence networks that was applied to capture the coevolution patterns within genomes of influenza viruses. To facilitate easy public use of this model, an R package ‘cooccurNet’ is presented here. Results ‘cooccurNet’ includes functionalities of construction and analysis of residues (e.g. nucleotides, amino acids and SNPs) co-occurrence network. In addition, a new method for measuring residues coevolution, defined as residue co-occurrence score (RCOS), is proposed and implemented in ‘cooccurNet’ based on the co-occurrence network. Availability and Implementation ‘cooccurNet’ is publicly available on CRAN repositories under the GPL-3 Open Source License (http://cran.r-project.org/package=cooccurNet) Supplementary information Supplementary data are available at Bioinformatics online.