Phylogenomic profiling

As already mentioned in Network Clustering, Phylogenomic profiling is used to analyze the compositions of the clusters.

Note that when using Phylogenomic_Profiling.r, you will have to define an order of your input species at Line22. Better in a reasonable phylogenetic manner. Easier for you to observe the specific patterns.  

Below is an example of phylogenomic profiling of 62125 synteny clusters (of BUSCO genes) from 107 plant genomes (Zhao and Schranz 2019). 

Zhao, T., & Schranz, M. E. (2019). Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes. Proceedings of the National Academy of Sciences, 116(6), 2165-2174.