A reviewer has commented the following on a whole-genome snp-tree + gene gain/loss hierarchical tree (generated with roary + pvclust):

" It would be better to first count insertion events rather than total number of genes and it is important to maintain a clear connection to the SNP-generated tree. "

Could someone suggest how to identify these 'insertion events'? Does this refer to horizontal gene transfers? Recombinations? Is there a webtool preferably that can identify such events?