A tooL for Prokaryotic Phylogeny And Clustering Analysis (ALPPACA) is a pipeline that allows both de-novo and reference-based phylogenetic analysis of prokaryotic genomes. The pipeline provides a suite of analyses tailored for different scenarios, designed to allow analysis of datasets represented by three different genetic diversity levels, all in one package. These levels of similarity influence ...

Klebsiella pneumoniae is a well-studied human pathogen for which antimicrobial resistant and hypervirulent clones have emerged globally. K. pneumoniae is also present in a variety of environmental niches, but currently there is a lack of knowledge on the occurrence and characteristics of K. pneumoniae from non-human sources. Certain environmental niches, e.g., animals, may be associated with high ...