syntenet: an R/Bioconductor package for the inference and analysis of synteny networks

ABSTRACT Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny analyses. Here, we present syntenet , an R package to infer and analyze synteny networks from whole-genome protein sequence data. The package offers a simple and complete framework, including data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Graphical functions are also available to create publication-ready plots. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate. Availability and Implementation The package is available on Bioconductor ( https://bioconductor.org/packages/syntenet ), and the source code is available on a GitHub repository ( https://github.com/almeidasilvaf/syntenet ).