syntenet

An R/Bioconductor package for the inference and analysis of synteny networks

Summary

The goal of syntenet is to infer synteny networks from whole-genome protein sequence data and analyze them. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform:

• Synteny detection using a native implementation of the MCScanX algorithm, a C++ program that has been modified and ported to R with Rcpp. This way, users do not need to install MCScanX beforehand, because syntenet has its own implementation of the same algorithm.
• Synteny network inference by treating anchor pairs as edges of a graph;
• Network clustering using the Infomap algorithm;
• Phylogenomic profiling, which consists in identifying which species contain which clusters. This analysis can reveal highly conserved synteny clusters and taxon-specific ones (e.g., family- and order-specific clusters);
• Microsynteny-based phylogeny reconstruction with maximum likelihood, which can be achieved by inferring a phylogeny from a binary matrix of phylogenomic profiles with IQTREE.