Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually
attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that …

In this perspective, we explore the transformative impact and inherent limitations of
metagenomics and single-cell genomics on our understanding of microbial diversity and …

Motivation Phylogenetic placement of a query sequence on a backbone tree is increasingly
used across biomedical sciences to identify the content of a sample from its DNA content …

Using k-mers to find sequence matches is increasingly used in many bioinformatic
applications, including metagenomic sequence classification. The accuracy of these …

Consider comparing a sequencing read of unknown origin to a set of reference genomes.
This problem underlines many applications, including metagenomic analyses. The exact …

Inference of species trees plays a crucial role in advancing our understanding of
evolutionary relationships and has immense significance for diverse biological and medical …

Abstract African Swine Fever Virus (ASFV) poses an ongoing threat with widespread
outbreaks affecting both domestic and wild pig populations globally. Effective management …

Motivation The study of viral and bacterial species requires the ability to load and traverse
ultra-large phylogenies with tens of millions of tips, but existing tree libraries struggle to …

The advent of CRISPR-Cas9 genome editing technologies has spurred the development of
large-scale cell lineage tracing systems. These techniques involve integrating synthetic DNA …

Using k-mers to find sequence matches is increasingly used in many bioinformatic
applications, including metagenomic sequence classification. The accuracy of these …