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A phylogeny is a hypothetical reconstruction of the evolutionary relationships of a group of organisms or a set of sequences (nucleotide or amino acid). Phylogenies are often represented graphically in the form of a 'tree' and enable scientists to find new relationships between organisms.
CONIPHER is a computational framework for accurately inferring subclonal structure and the phylogenetic tree from multisample tumor sequencing, accounting for both copy number alterations and mutation errors.
The diversity and spillover potential of pangolin-associated microbes are not fully understood. Here, the authors describe the distribution and spectrum of reported pangolin microbes by integrating data from multiple sources and assess their potential to emerge as human pathogens.
Invasive Salmonella Typhimurium bloodstream infection causes a significant public health burden in sub-Saharan Africa. Here, the authors analyse whole genome sequences of 1,302 S. Typhimurium isolates from Africa and describe its evolution, geographic spread, and antimicrobial resistance characteristics.
The concept of reference frames inspires researchers to develop a differential ranking system for measuring relative differential abundance, which does not require information about absolute microbial load.
Complementary genomic frameworks for taxonomic classification of viruses infecting bacteria and archaea reveal evolutionary drivers, mosaicism and perspective on the genetic diversity of the tiniest, most abundant biological entities on Earth.
