Daniel Wilson, one of the CRyPTIC partners, has recently published a paper where he introduces a new approach, genomegaMap, which estimates the ratio of non-synonymous to synonymous mutations (usually referred to as dN/dS) at sites across the genome. This ratio can provide important clues to which parts of the genome are under selection pressure, which can lead to, amongst other things, antibiotic resistance.
GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 GenomesDaniel J Wilson and the CRyPTIC Consortium
Mol. Biol. Evol. 37(8):2450–2460
The paper is free to download and can be accessed here.