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 …

Over the last 10 or more years, there has been a tremendous increase in the use of
computational techniques (many of which come directly from biology) for estimating …

Recent algorithmic advances in amplicon-based microbiome studies enable the inference of
exact amplicon sequence fragments. These new methods enable the investigation of sub …

The global diversity of Bacteria and Archaea, the most ancient and most widespread forms
of life on Earth, is a subject of intense controversy. This controversy stems largely from the …

Background Likelihood-based phylogenetic inference is generally considered to be the most
reliable classification method for unknown sequences. However, traditional likelihood-based …

We present an evolutionary placement algorithm (EPA) and a Web server for the rapid
assignment of sequence fragments (short reads) to edges of a given phylogenetic tree under …

Different regions of the bacterial 16S rRNA gene evolve at different evolutionary rates. The
scientific outcome of short read sequencing studies therefore alters with the gene region …

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 enormous complexity of biological systems at the molecular level must be answered
with powerful computational methods. Computational biology is a young field, but has seen …

The free‐living (FL) and particle‐attached (PA) marine microbial communities have
repeatedly been proved to differ in their diversity and composition in the photic ocean and …