Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

摘要: Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess nine three important scenarios: divergence, lateral genetic transfer (LGT) and rearrangement. Among these, are most sensitive extent less low moderate frequencies LGT, robust against We describe application well-studied empirical datasets, introduce a new jackknife node support. Our results demonstrate that phylogenomics computationally scalable multi-genome can generate biologically meaningful phylogenies insights into evolution.