syntenet

Inference And Analysis Of Synteny Networks

Bioconductor version: 3.23 · Package version: 1.14.0

syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("syntenet")