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Add Rcpp or RcppArmadillo integration to an R package for high-performance C++ code. Covers setup, writing C++ functions, RcppExports generation, testing compiled code, and debugging. Use when an R function is too slow and profiling confirms a bottleneck, when you need to interface with existing C/C++ libraries, or when implementing algorithms (loops, recursion, linear algebra) that benefit from compiled code.

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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-bas

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