Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …

Shotgun metagenomics and computational analysis are used to compare the taxonomic and
functional profiles of microbial communities. Leveraging this approach to understand roles of …

Background Microbiome studies often involve sequencing a marker gene to identify the
microorganisms in samples of interest. Sequence classification is a critical component of this …

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome
data, but a lack of consensus about benchmarking complicates performance assessment …

In order to determine the role of the database in taxonomic sequence classification, we
examine the influence of the database over time on k-mer-based lowest common ancestor …

A comprehensive account of both basic and advanced material in phylogeny estimation,
focusing on computational and statistical issues. No background in biology or computer …

The effective use of metabarcoding in biodiversity science has brought important analytical
challenges due to the need to generate accurate taxonomic assignments. The assignment of …

Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and
interpret the tsunami of metagenomic sequencing data generated by high-throughput …

Genetic tools are increasingly used to identify and discriminate between species. One key
transition in this process was the recognition of the potential of the ca 658bp fragment of the …

Recent advances in the field of meta-omics sciences and related bioinformatics tools have
allowed a comprehensive investigation of human-associated microbiota and its contribution …