Multiple sequence alignments are an essential tool for protein structure and function
prediction, phylogeny inference and other common tasks in sequence analysis. Recently�…

Motivation: Biological sequence data is accumulating rapidly, motivating the development of
improved high-throughput methods for sequence classification. Results: UBLAST and�…

We describe MUSCLE, a new computer program for creating multiple alignments of protein
sequences. Elements of the algorithm include fast distance estimation using k mer counting�…

Abstract Motivation The 16S ribosomal RNA (rRNA) gene is widely used to survey microbial
communities. Sequences are often clustered into Operational Taxonomic Units (OTUs) as�…

Background In a previous paper, we introduced MUSCLE, a new program for creating
multiple alignments of protein sequences, giving a brief summary of the algorithm and�…

Motivation: Chimeric DNA sequences often form during polymerase chain reaction
amplification, especially when sequencing single regions (eg 16S rRNA or fungal Internal�…

Motivation: Next-generation sequencing produces vast amounts of data with errors that are
difficult to distinguish from true biological variation when coverage is low. Results: We�…

Metagenomics experiments often characterize microbial communities by sequencing the
ribosomal 16S and ITS regions. Taxonomy prediction is a fundamental step in such studies�…

Amplified marker-gene sequences can be used to understand microbial community
structure, but they suffer from a high level of sequencing and amplification artifacts. The�…

Land plants associate with a root microbiota distinct from the complex microbial community
present in surrounding soil. The microbiota colonizing the rhizosphere (immediately�…