RPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree.

ABSTRACT: The ability to distinguish different circulating pathogen clones from each other is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low-variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral

SUBMITTER: Wailan AM 

PROVIDER: S-EPMC6521585 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature